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Renegade Splinter Faction

 Renegade Splinter Faction
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Basically, a group who decides to Start My Own and separates from a larger organization — holding the main beliefs or goals of the original, but are wholly or mostly evil.
Three common ways of applying this trope:
The writer doesn't want to portray some organization, nation, or religion as entirely evil. It may be a real-world institution or an institution from this fictional world that was previously described as at least semi-decent. But the author still wants villains belonging to it, so they invent a renegade group.
A faction that operates without authorization, and their methodology differs from the main body. Often they are extremists: escalating a conflict, willing to break the rules, far more infamous than their mother alignment — but this isn't always the case.
A faction that crosses Pragmatic Villainy lines that would, in Real Life, invite massive retaliation.
Note that it doesn't apply to out-and-out turncoats: the faction must still keep the general ideas of the original; only with less benevolent policies. It may, however, adhere to ideals that the original faction has abandoned. If the factions are religious in nature, related to The Heretic. Can result in Enemy Civil War. Renegade Russian is a common nation-specific subtrope since Russians and Soviets get this treatment especially often. If the original organization was bad-ish, but not bad enough, this may result in The Good, the Bad, and the Evil. This may be used to provide an inversion of My Species Doth Protest Too Much by setting up an antagonist, then revealing that the rest of their faction doesn't like them either.
For the individual version, see Rogue Agent. A major source of Terrorists Without a Cause.
Compare La Résistance.
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Star Trek Online:
The True Way Alliance serves as a justification for having Cardassian and Jem'Hadar enemies in the game without conflicting with the ending of Deep Space Nine, in which the Dominion and Cardassian Union made peace with the Federation, Klingons, and Romulans and the Cardassians acquired a civilian-ruled government. The True Way are terrorists who want to restore the old military regime and resume the Dominion War.
Inverted with the Romulan Republic, the faction for Romulan player characters. They broke away from the Romulan Star Empire after the Hobus supernova and Empress Sela and the Tal Shiar seizing control and are a democratic polity that just wants to rebuild Romulan society in peace.
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 Star Trek Online (Video Game)
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Mobile Suit Zeta Gundam: Though officially part of the Earth Federation serving as a special security force, the Titans are used by a corrupt politician to gain control of the Earth Sphere. Their actions are zealous, including gassing an entire colony. Eventually, they go full renegade after they're exposed by the AEUG.
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Guild Wars 2 has this for every player race: Humans fight the zealous White Mantle. Charr have the dogmatic Flame Legion. Asura compete with the amoral Inquest. Sylvari fight the alien Nightmare Court. Nords struggle against the vicious Sons of Svanir. In addition, the Renegades and Separatists are Charr and human factions whose hatred for the other race was so intense that they refused to abide by the peace treaty between their people. They are now openly hostile to anyone not a member of their faction and wage guerilla warfare against their racial enemies and the "traitors".
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Sonic the Hedgehog (Archie Comics): Unlike the other Freedom Fighters, the Sand Blast City Freedom Fighters are ruthless and their actions questionable. It was because of their abusive treatment out of Fantastic Racism that the deroboticized Robians of Sand Blast City joined the Eggman Empire. Yes, it got so bad that the former slaves entered into an alliance with their former master.
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This happens to Team Plasma in Pokémon Black 2 and White 2. N's Plasma just wants people to stop using Poké Balls, though they're still on the 'release your Pokémon' kick. Ghetsis' group wants to take over Unova.
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 Pokémon Black 2 and White 2 (Video Game)
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Dragon Age:
Templar Order separates itself from the Chantry following the events of Dragon Age II to wage war on the mages on their own. By the time of the sequel, smaller Templar factions have split from the order and turned to banditry in the Hinterlands, and they were disavowed by their leaders.
Dragon Age: Inquisition had two separate splinter factions serving as the Big Bad's enforcers:
The Venatori, a terrorist organization originated from the Tevinter Imperium that have pledged their allegiance to the Elder One and aim to sow chaos in Southern Thedas. It's stressed by Dorian that these individuals do not represent Tevinter or its values, though he cynically points out that some fellow Magisters do agree with them in private. The current leader of the Imperium, Archon Radonis, doesn't like them either, as he enlists the Inquisition's help to root them out and employs a mage-killer to assassinate Venatori leaders.
The Red Templars, who have turned to consuming red lyrium to gain immense power at expense of sanity, are also another splinter faction from the Templar Order. The irony is that in other circumstances, this group and the Venatori would have easily been enemies since the Templars were an organization devoted to fighting and containing mages, specially ones from Tevinter, who have a sinister reputation on Southern Thedas.
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The House of Dusk: An inversion. The House of Dusk was created when the various rival factions of Fallen from the first game consolidated, pooling their resources for survival.
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 Destiny (Video Game)
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Fëanor and his sons and followers in The Silmarillion are more or less a Renegade Faction of the High Elves.
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 The Silmarillion
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In the "Season of Infamy" DLC in Batman: Arkham Knight, the League of Assassins has split into two opposed factions, with the main faction still loyal to the barely-alive Ra's al Ghul while the splinter faction is led by his daughter Nyssa Raatko. If Batman makes the "Destroy the cure" choice at the end of the sidequest, which condemns Ra's to death in at most a few days, Nyssa takes over the League entirely and takes it out of Gotham forever.
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 Batman: Arkham Knight (Video Game)
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Alias: SD-6 works as a sometimes-splinter group of the Alliance of Twelve, since its head Arvin Sloane has his own agenda apart from the Alliance.
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 Alias
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Angel: Two morally gray characters in Solitary Man belong to a group that split off from the Watchers due to believing that they needed to fight evil themselves rather than rely on the Slayer. The principle is an admirable one, but they also think that more people should be Killed to Uphold the Masquerade.
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In The Legend of Zelda: Breath of the Wild, the Yiga Clan are a splinter faction of the Sheikah who could not forgive Hyrule rejecting them. As a result, they've thrown in their lot with Calamity Ganon and serve as recurring enemies for Link.
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Star Trek: Enterprise:
The Suliban Cabal is a terrorist faction that seeks to alter the timeline. Because of Star Trek's tendency to lump the same species into one group, many assumed that all Suliban were bad. It turns out that the Cabal is just a renegade group.
The xenophobic Terra Prime commits terrorist acts so that humanity will adopt an isolationist stance.
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The Expanse: Each of the three main factions of the show has these, to greater and lesser degrees:
Earth has the Protogen Corporation, which doesn't really care about Earth at all and was merely selling out to the highest bidder, as they are practically a fourth party non-government mega-corporation. Heck, Protogen outright turns on its UN allies in Season 2 and tried to sell out to rogue elements of the Martian government, only to then be browbeaten back into working for the UN. Presumably, the only reason Protogen didn't try to sell the proto-molecule to the OPA is because the Belters couldn't afford it.
The UN also features a cabal of hardliners led by Undersecretary Errinwright who conspire with Protogen in order to gain an advantage in their Space Cold War with Mars. While they initially seem to share the same goals as Protogen, they differ in that they are wholly dedicated to ensuring that Earth remains the dominant power in the solar system at all costs.
Similar to Earth, the Martian Congressional Republic also features hardliners who actively seek to escalate tensions between Earth and Mars. After learning about the proto-molecule, they gleefully allow Protogen to slaughter Martian marines in a test run of the hybrid weapons. After several seasons of subtle buildup and background references, in Season 5 they overtly break off from Mars to found the Laconia faction, absconding with a third of the MCRN's fleet (or rather, what remains after their losses in the recent war with Earth) to settle on a new colony world beyond the Ring.
This is a major issue with the OPA, which isn't really a unified organization so much as an idea/movement. Word of God compares them to real-life revolutionary movements like the Irish Republican Army, with each terrorist cell claiming to be the "real" OPA, though they can occasionally be browbeaten together to act towards a unified goal. Fred Johnson's powerful faction based on Tycho Station is trying to establish the OPA as a legitimate government diplomatically recognized by Earth and Mars, and while Johnson would like to acquire long-range nuclear weapons and/or the proto-molecule, he only wants them as deterrents to establish balance of power. Other groups are outright terrorists carrying out targeted assassinations, such as the "Black Sky" cell, and the more extreme Ceres cell led by Anderson Dawes. Then there's Marco Inaros's small but utterly ruthless "Free Navy", who are so radical that they basically are a Renegade Splinter Faction compared to the other collective OPA factions. The distinction is that while Dawes is an extremist, pro-war politician, he's still a politician, and can be negotiated with if it serves his own interests (grudgingly deciding to ally with Johnson to explore the Ring in Season 3 so the OPA can present a united front against Earth and Mars). In contrast, Inaros is just a fanatical Blood Knight. In Season 5, Inaros forces all the other factions to unite under the Free Navy through sheer ruthlessness, hostage-taking, and outright assassinating both Johnson and Dawes, to the point that by the season finale "OPA" and "Free Navy" are being used synonymously. They even enter into an alliance of convenience with Laconia, the hardliner Mars splinter faction. But then in Season 6, Inaros' growing instability leads to an Anti-Mutiny situation, with Johnson's former second-in-command Camina Drummer rallying a growing number of OPA ships as a splinter faction back from the Free Navy and allying with the Earth-Mars joint fleet.
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 The Expanse
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When Sirius is blockaded by the Terran Treaty Organization, a portion of their military which was off-planet at the time escapes and goes rogue, becoming terrorists. Especially years later when the Siriusi government capitulates and signs a peace treaty with TeTO, leading to the renegades denouncing them as traitors.
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 V (1983)
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Honor Harrington: The Faithful of the Church of Humanity Unchained who settled Masada, originally part of the Church of Humanity Unchained on the planet Grayson, broke from the main church over theological disputes. In contrast to the Grayson church, the Masadans are such extremists that they've rejected all of the New Testament. Splinters of the Masadan branch later appear, somewhere between this trope and Former Regime Personnel, Pure in Faith and the Church of Humanity Unchained (Defiant).
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Earth's Alien History:
When Sirius is blockaded by the Terran Treaty Organization, a portion of their military which was off-planet at the time escapes and goes rogue, becoming terrorists. Especially years later when the Siriusi government capitulates and signs a peace treaty with TeTO, leading to the renegades denouncing them as traitors.
The Race has to deal with a wave of terrorism by ultra-conservatives who despise the many progressive reforms made by the Empire ever since joining TeTO. At one point, they even try to assassinate the Emperor (who, it should be remembered, the Race view as a god).
Ronan and his forces break from the main Kree Empire in order to keep waging war on the Novan Empire despite the recent peace treaty between the two.
Scorponok's group of Decepticons, who refuse to accept peace with the Autobots and go rogue to keep fighting them and organic life.
When the Last-of-all-Cities (a Lost Colony of militant pre-Surak Vulcans) captures a TeTO ship, their leadership decides to reverse engineer the technology and plan a long-term strategy to reconquer Vulcan. A more radical faction, however, goes rogue with the ship, operating under the delusion that using it in a show of force will make both their government and Vulcan surrender to them.
The Amazons of Bana-Mighdall betrayed the rest of their people to serve the Goa'uld, on the grounds that the Greek Gods did nothing to aid them.
The Zhat Vash are disavowed by the Romulan government after their attempt to kill Hanka Kamiya and her Digimon partner, both to preserve relations with TeTO and because the government and its partners in the Pact of the Raptor don't share the group's hatred of digital lifeforms, instead seeing them as an asset.
A heroic (or at least A Lighter Shade of Black) example pops up among the Milky Way colonists in the Andromeda Galaxy, where David Xanatos uses the fact that he's the only member of The Illuminati present in this galaxy to start building up his own version of the organization, built along his ideals rather than those of the leadership back home. The heroic/morally grey part comes from the fact that his ideals are to use their secret control of society to do good, rather than for personal gain.
HYDRA was a splinter faction of the Illuminati formed by their members in the Axis nations, who felt that openly ruling through fascism was better than the main brotherhood's MO of using the facade of democracy, so broke away to take power for themselves.
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The second season of Agents of S.H.I.E.L.D. sees the conflict between two remnant S.H.I.E.L.D groups: Coulson's team, (semi-) officially appointed by Nick Fury himself to rebuild the agency in the aftermath of Captain America: The Winter Soldier and the first season's finale, and the "True S.H.I.E.L.D." led by Commander Gonzales, who (kind of hypocritically) sees Coulson's group as this (thanks to a severe case of Fantastic Racism and Well-Intentioned Extremism).
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Bloodborne: Byrgenwerth College broke up into three factions based on different ideas of how to contact the Great Ones. Byrgenwerth, under its original leader Provost Willem, focused on scientific investigation and gaining Insight, while School of Mensis explored necromantic rituals and the Healing Church (led by Willem's student Laurence) wanted to study the Old Blood. The Healing Church ultimately wound up the most widespread, founding a religion based on worshipping the panacea properties of the Old Blood in order to experiment on its use with the people of Yharnam.
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 Bloodborne (Video Game)
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The Teenage Mutant Ninja Turtles (1987) are an inversion of the trope. They were founded by Hamato Yoshi, a martial artist who was expelled from the Foot Clan and fled to America, whereas his rival took over the clan and drove them to evil. Coincidentallynote He's actually got that name from his practice of breaking wood planks, Hamato is now known as "Master Splinter".
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 Teenage Mutant Ninja Turtles (1987)
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Star Trek: Picard: The antagonists of Season 3 are revealed to be a group of Changelings who broke off from the Great Link due to refusing to accept the peace treaty at the end of the Dominion War, and have been working to infiltrate and undermine the Federation ever since. They're in fact so renegade that they establish an alliance with the Borg to enable the latter's assimilation of Starfleet.
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Command & Conquer: Generals:
One mission has a renegade Chinese army (allied with the Middle Eastern Terrorists who are the game's main antagonists) as one of the enemies. In this game, China is one of the "good" factions.
The final U.S. mission in Zero Hour has the player allying with the GLA against Dr. Thrax, whose use of bioweapons disturbs even them. The first GLA missions focused on it reforming by defeating splinter factions led by the likes of Stealth Expert Prince Kassad.
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Valkyria Chronicles III: After a peace accord is signed between the Autocratic East Europan Imperial Alliance and the Principality of Gallia, the former's all-Darcsen Calamity Raven legion (whose members cared little for the Empire to begin with) become this, as they decide to go to extreme length for a chance to establish an independent Darcsen nation by attempting to activate a Valkyrian Pointless Doomsday Device as their trump card, with their first intended target being the Gallian capital. The game's Final Battle revolves around the heroes fighting to prevent the last of Calamity Raven from firing said Doomsday Device.
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In The Flash, the Trickster (during a time when he's an FBI agent) recruits fellow reformed Rogues (Pied Piper, Heat Wave, Magenta) into a strike force with one purpose: to hunt down the rest of the Rogues. This culminates in the Rogue War storyline. Eventually, Trickster and Heat Wave — actually victims of a Heel–Face Brainwashing Retconnote Pied Piper is also affected, but The Power of Friendship with the Flash overrides that — are Easily Forgiven and welcomed back into the "main" Rogues.
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Once working for the government, the eponymous Delta Green illegally continues its operations to defend America from the Cthulhu Mythos. Unsurprisingly, they also subvert the usual evil nature of the trope, even though they are often quite ruthless — understandably, considering the alternative.
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In the fourth Volume of RWBY, two representatives of the White Fang in Menagerie, Corsac and Fennec Albain, tell the former leader, Blake's father Ghira, that the assault on Beacon Academy was due to the actions of Adam Taurus's sect of the White Fang, who they claim has abandoned the management style of the main organization led by High Leader Sienna Khan. Volume Five reveals that they were telling the truth; however, Corsac and Fennec themselves are both secretly allied with Adam, who proceeds to assassinate Khan and take over the mainline White Fang himself.
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While many secret societies in Paranoia are actually created by the Computer to provide an outlet for rebellious tendencies, they tend to develop splinter groups from time to time.
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The Order of the Emerald Claw in Eberron are an outcast Karrnathi military order who actually serve Erandis d'Vol, leader of the Blood of Vol. Most of them do, admittedly, believe they serve Karrnath, but they're functionally independent at this point and the Karrnathi government has declared them traitors in a very genuine, non-Xanatos Gambit sort of way.
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The Amazons of Bana-Mighdall betrayed the rest of their people to serve the Goa'uld, on the grounds that the Greek Gods did nothing to aid them.
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Several episodes of Highlander involve a splinter faction of the Watchers who have decided to exterminate immortals instead of watching them.
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Dragon Age: Inquisition had two separate splinter factions serving as the Big Bad's enforcers:
The Venatori, a terrorist organization originated from the Tevinter Imperium that have pledged their allegiance to the Elder One and aim to sow chaos in Southern Thedas. It's stressed by Dorian that these individuals do not represent Tevinter or its values, though he cynically points out that some fellow Magisters do agree with them in private. The current leader of the Imperium, Archon Radonis, doesn't like them either, as he enlists the Inquisition's help to root them out and employs a mage-killer to assassinate Venatori leaders.
The Red Templars, who have turned to consuming red lyrium to gain immense power at expense of sanity, are also another splinter faction from the Templar Order. The irony is that in other circumstances, this group and the Venatori would have easily been enemies since the Templars were an organization devoted to fighting and containing mages, specially ones from Tevinter, who have a sinister reputation on Southern Thedas.
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Cycles Upon Cycles has a few examples:
The Heretic Geth, as per canon. Reinforced by the main Consensus making peace with the Quarians and joining the Alliance early on.
A faction of the Krogan, enraged over the bulk of the species voluntarily being absorbed by the Zerg, breaks off and goes their own way.
When the Quarians are first joining the Alliance, a movement starts up opposed to both this and the peace with the Geth. Later, they go outright rogue, with plans to conquer their people and enslave the Geth.
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Mobile Suit Gundam 00 provides several examples:
La Eden, a violent right-wing political group within the AEU (though not supported by the superpower), commits a series of terror attacks to stop the protagonists. Celestial Being responds by simultaneously curb-stomping the entire faction.
Team Trinity claims to be part of Celestial Being, sharing the similar technology and goal of eliminating warfare. However, the Trinities are much more ruthless, attacking without provocation or mercy. Eventually, the two groups come into conflict.
The Innovators are originally part of Celestial Being, but thanks to the events of Season 1, the two groups splinter, with the Innovators causing most of the problems for the next season.
Splintering off from the Federation military, the ESF Coup detat Faction seeks to expose the A-Laws' atrocities. Like the Trieze Faction, their going "renegade" makes the Earth Sphere Federation come off as increasingly antagonistic.
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The Lost Room has Karl Kreutzfeld and his Mooks. As it turns out, Kreutzfeld used to be a member of the Legion. While members of the Legion tend to avoid killing in order to acquire Objects, Kreutzfeld and his cronies have no such compunctions.
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Attack on Titan:
The Survey Corps becomes this for the royal government after they send the Military Police's Central 1st Brigade to execute The Purge of the Survey Corp after the King and the government see them as becoming too powerful and closer to the truth.
The Yeagerists are a faction that believes their commanders and the military junta of Paradis is not doing enough to protect the island, and only Eren Yeager can save them from the threat Paradis faces. They proceed to free Eren from prison and execute a coup against the military junta. Most of their members are defectors from the Survey Corps, disgruntled with Hange Zoe's leadership.
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Coruscant Nights has a secondary character, Laranth Tarak, who before the Jedi Purge was a member of the Gray Paladins, a Jedi sect considered heretical by the Jedi Council mainly for preferring blasters to lightsabers.
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The Glove of Darth Vader:
The Empire is presented as being headed by the Central Committee of Grand Moffs, with Trioculous as a Puppet King and the Prophets of the Dark Side being the ones really pulling the strings. While this series was poorly received and mostly rendered Canon Discontinuity, later supplemental material shoehorned it back into continuity with some handwaving, the most prominent case being that this Imperial faction was actually a splinter that broke away from the central government on Coruscant, which was at the time under the control of Ysanne Isard and her pawns on the Imperial Ruling Council according to the X-Wing Series.
The aforementioned Prophets of the Dark Side are actually this twice over, as the same supplemental materials that retconned the Central Committee as a splinter faction reveal that they're not the real Prophets (which are a legitimate Dark Side cult recruited by Palpatine) but a bunch of fraudulent imposters established by Imperial Intelligence to act as a Propaganda Machine, only to eventually go rogue by means of setting up the Committee as their puppets to take over the Empire for themselves. Since Isard is Director of Imperial Intelligence, this means they're not just defying her pawns but her directly.
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In Patriot Games, the Ulster Liberation Army is a Maoist splinter faction of the (Marxist-Leninist) Provisional IRA. Naturally, the ULA is more ruthless than the group they left.
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SCP Foundation: Shortly after the Foundation's establishment, the 05 Council approved a black ops group of soldiers to conduct missions deemed too dirty for the Foundation to publicly conduct and designated them "The Insurgency". But after some time, the group went rogue and defected from the Foundation, becoming the Chaos Insurgency, a group of interest who seek to weaponize anomalies.
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Early in Rogue One, Mon Mothma tells Jyn Erso that her Parental Substitute Saw Guererra broke off from the rest of La Résistance because his ways were considered too extreme.
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In the Discworld novels set after Small Gods, the Omnian church schisms on a daily basis. The scary fanatical ones who want to go back to the days of Vorbis are named in The Science of Discworld IV: Judgement Day as the Church of Latter-Day Omnians.
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Nextwave splits itself off from H.A.T.E. when they learn that H.A.T.E. is actually owned by the Beyond Corporation, which is a cover group for S.I.L.E.N.T., their ostensible nemesis. Nextwave tries to do good when they're not on the run from their employers.
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Mission: Impossible – Fallout has the Apostles, formed by remnants of the Syndicate following the defeat of Solomon Lane in the previous film and are now under the payroll of a mysterious fundamentalist named John Lark.
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There's also the Midwestern Brotherhood in the semi-canonical Fallout Tactics: Brotherhood of Steel. Unlike the main Brotherhood, they have been forced to recruit all-comers from the surrounding areas, eventually even including intelligent Deathclaws, due to many of them dying, when their airships crashed and all contact with the Main Brotherhood was lost. While they're less benevolent than the DC Brotherhood, they are still forced to become protectors of the surrounding area in order to maintain their flow of new recruits and to fight the Calculator's Mecha-Mooks. Of course, the whole reason they were sent out in airships in the first place was that they were already a dissenting faction, claiming that the Brotherhood should extend its mandate to protecting people and open up its membership.
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The Lieutenant of Inishmore: Padraic joined the INLA, a splinter faction of the IRA, after the IRA threw him out for being too psychotic. He is also planning on starting his own splinter group because he doesn't like that the INLA doesn't stop the drug dealers they "protect" from selling drugs to Catholics (not to mention that the INLA think he's too psychotic for them too and would be happy to see the back of him). Plentiful discussion is made of the "splinter group of a splinter group" idea.
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In Mobile Suit Gundam Wing: Endless Waltz, it's revealed that the Gundam pilots have split from the Barton Foundation. Disagreeing over the goal of world conquest, the pilots decide to focus on stopping OZ instead.
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Patriot Games: As in the novel, the Ulster Liberation Army is an offshoot of the Provisional Irish Republican Army. In the movie, they're unnamed, though, and it goes even further: they kill/snitch on IRA members, as O'Donnell does to a couple of hitmen in one scene, and Annette during sex with another IRA member. At one point, Ryan himself refers to the group as an "ultra-violent faction of the IRA, fighting the cause their way".
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Van Helsing (2016): Season 4 reveals that Harrison's operation in Season 2, which created the Daywalkers for no other reason than because they could, was rogue from the main Blak-Tech organization, which is dedicated to protecting what's left of humanity from the vampires.
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Supergirl (2015): Project Cadmus starts out as a severely off-books black-ops U.S. government organization that is obsessed with persecuting aliens and is even willing to harm normal humans who get in their way. By Season 2, however, they've gone outright rogue, carrying out terrorist attacks armed with alien weaponry, in order to prove that aliens are the true threat. Additionally, the leader of Cadmus is revealed to have a personal score to settle with aliens in general and Supergirl in particular. The leader is Lex Luthor's mom, who thinks that her son was unjustly imprisoned for only wanting to show the danger posed by aliens, specifically Superman.
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The main bad guys in Star Trek: Bridge Commander are a rogue Cardassian faction who have found a powerful new race and are tricking them into building the faction powerful ships, as well as the technology to make stars go boom.
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Hellsing Ultimate Abridged depicts Maxwell and his army of crusaders as an extremist splinter faction of the Catholic Church, contrasting from the source material.
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In Star Trek (2009), when Captain Pike confronts the Narada, he states that the Federation and the Romulan Star Empire are not at war with each other. However, Nero replies that his crew does not represent the Empire, as they "stand apart", which is the truth: in Nero's time, there isn't much left of the Romulan Star Empire, as Romulus and Remus were wiped out by a supernova.
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The Second Imperium from the Young Jedi Knights was retconned to be one of these because the later-published but chronologically-earlier Hand of Thrawn duology established that Pellaeon had successfully established peace between the main Imperial Remnant and the New Republic several years before Young Jedi Knights takes place.
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The third book in The Flight Engineer reveals that the Fibians that have been helping the Mollies fight the Commonwealth are under the command of a renegade queen. Fleeing their pursuit, Peter Raeder and his crew blunder into contact with the Fibian central government, which after some deliberation decides to come to the rescue.
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The bad guys in Guardians of the Galaxy (2014) are led by Ronan, a religious extremist rogue allying with a bigger evil. His original faction basically disavows him, telling the people he attacked that he's their problem now.
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Metal Gear:
For a time, the Patriots were the American faction of the original Philosophers. The truth is a little more complicated; there was a splintering of the Philosophers when the Wisemen's Committee died off, with the American, Chinese, and Russian groups breaking off from one another. The conflict in Metal Gear Solid 3: Snake Eater led to the rise of the American branch. However, by Metal Gear Solid: Portable Ops, Zero was tired of the Philosophers' bickering, so he stole back the other half of the Philosophers' Legacy and reformed the group into the Patriots.
In Metal Gear Solid, FOXHOUND — originally an advanced special forces unit — goes rogue and takes over a research base holding nuclear weapons and the means to launch them, kidnapping the DARPA Cheif and ArmsTech President. This is especially bad since FOXHOUND would have been the go-to unit to solve this sort of situation if they weren't the ones creating it! Instead, former FOXHOUND operator Solid Snake is asked to save the world by his old friend and former FOXHOUND commander, Colonel Campbell.
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XCOM: Chimera Squad has groups of rogue XCOM troops who once ran security for City 31 who have become mercenaries for the various factions you face throughout the game, many of whom have Fantastic Racism against Earth's new alien populace and resent XCOM for both for integrating humans and aliens and for establishing a peaceful, democratic government rather than leading a "conquest of the stars" as Kelly puts it. They're actually members of Shrike, a much larger organization comprised mostly of renegade XCOM members who were manipulating the other factions, inciting them to cause trouble in the hopes that it would push XCOM to resort to more drastic measures to defeat them. Their ultimate goal is to install a military government similar to ADVENT and reignite the war against the Ethereals and their empire. Funnily enough, despite their Fantastic Racism, there's actually a fair few aliens among their ranks as well. That's because they're not actually anti-alien. This is simply a cover story so their operatives can pose as racist washouts and members of the local anti-alien movements. In reality, they're completely fine with their new alien neighbors, they simply wish for a return to military rule. Many aliens who otherwise despised ADVENT still prefer a military dictatorship to democracy, and view XCOM as a preferable alternative ruling organization.
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Stargate-verse:
Stargate SG-1:
The rogue NID is this for Earth. While the regular NID is rather shady, the renegade group turns outright criminal, stealing technologies that the SGC fails to negotiate for from other planets, including from Earth's allies the Tollans and the Asgard. Eventually, the rogue NID finally splinters off into the Trust once their wealthy backers are arrested. Freed from any government restrictions, the Trust becomes even more violent, conducting chemical attacks and assassination. When their operatives are driven away from Earth by the SGC, the group manages to get themselves captured and implanted with Goa'uld. Ironically, Ba'al and Athena end up in charge of the Trust and head several major corporations.
In one second-season episode, the SGC encounters a species of aliens called the Reetou who exist out-of-phase from the rest of the universe (read: they're invisible) and were mostly exterminated by the Goa'uld because proximity gives the snakes headaches. One faction of Reetou decided to exterminate the Goa'uld, and that the best way to do it was a scorched-Earth (pardon the pun) policy against humanity, whom the Goa'uld use as hosts. The Reetou Central Authority found this reprehensible and sent an agent to Earth to warn the SGC.
Good/evil-flipped with the Ancients, a splinter group from their progenitor race the Ori; the Ancients believe that Sufficiently Advanced Aliens should not play God, whereas the Ori believe that they should, having learned to draw power from mortals' worship of them.
Stargate Atlantis:
After Michael is rejected by his fellow Wraith for being a Half-Human Hybrid, he goes off on his own and forcibly turns a large group of humans into hybrids like him, while also modifying himself so that he doesn't need to feed on humans anymore (freeing himself from this weakness). His goal is to destroy both the humans and the Wraith, establishing the hybrids as the dominant race in the Pegasus Galaxy. In a Bad Future, he succeeds.
Atlantis also introduces the Vanir, a rogue group of Asgard, who believe that their species must survive at any cost, up to and including experimenting on humans to solve their Clone Degeneration problem. Millennia ago, they split off from the larger Asgard group and left for the Pegasus Galaxy, where they started experimenting on humans without any oversight. In modern times, they are perfectly willing to cause untold destruction across the galaxy in order to keep the Wraith contained. When they find out that their Asgard cousins have all died out, it only serves as proof to them that they were right all along.
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Shadows over Meridian:
The Snowpoint arc has an interesting example wherein most of the faction doesn't know that they're renegade: when Elyon orders her northern army to end the siege of Snowpoint and withdraw to the capital to regroup, Vera Bexley refuses to abandon her quest for revenge on the Mogriffs and goes rogue, tricking her friends into believing that they've been ordered to go on a covert mission to assassinate the Mogriff leader Metalbeak (the main target of Vera's vendetta).
The Swamplands arc features a more clearcut example with the rebel forces in the titular region. Under the command of Lord Kur, these rebels have cut off communication between the region and the capital (with help from Aldarn, who agrees with their aims but not their motives) so that they can act without oversight from Elyon or any more reasonable rebel leaders who would be opposed to them unilaterally rounding up suspected Phobos loyalists without trial, or their intentions of purging all nonhumans from the area. It says something that the locals are actually happy to have Phobos swoop in and defeat the rebels, as his rule of the area was at least more peaceable by comparison.
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Marvel Universe:
HYDRA was initially this for Nazi Germany, created due to the desire to maintain the relevance of Captain America and other wartime heroes in spite of the Wartime Cartoon Values Dissonance. This has created historical acknowledgement issues of its own, particularly in The Avengers: Earth's Mightiest Heroes: World War II ended up depicted as being waged mostly against Hydra while the Nazis are relegated to a Historical In-Joke. Hydra itself has had several splinter groups: A.I.M., the Hand (although the Hand consider themselves to be the originals and Hydra the splinter group), and the Secret Empire, among others.
Nextwave splits itself off from H.A.T.E. when they learn that H.A.T.E. is actually owned by the Beyond Corporation, which is a cover group for S.I.L.E.N.T., their ostensible nemesis. Nextwave tries to do good when they're not on the run from their employers.
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In Operation: S.O.U.L.M.A.T.E., the Splinter Cell broke off from the main Kids Next Door a long time ago and was responsible for the deaths of many adults, carrying out the Bojinka Attacks.
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In Captain America: The First Avenger, HYDRA and the man who became the Red Skull fall out with Nazi Germany early on, although unlike many examples of this trope, it seems that he had his own agenda all along rather than splitting off over ideological differences that cropped up later. Subverted when Agents of S.H.I.E.L.D. established that HYDRA predated the Nazis by centuries and were just using them.
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The Owl House: The first organized La Résistance against Emperor Belos — as opposed to just the protagonists' antics — are the Bards Against The Throne (aka "the BATTs"), a group of Bard Coven members, including Head Witch Raine Whispers, who have gone rogue in order to oppose Belos' tyranny. Late in Season 2, they join with members of other covens, rebranding as the Covens Against The Throne (aka "the CATTs").
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The Race has to deal with a wave of terrorism by ultra-conservatives who despise the many progressive reforms made by the Empire ever since joining TeTO. At one point, they even try to assassinate the Emperor (who, it should be remembered, the Race view as a god).
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The rogue NID is this for Earth. While the regular NID is rather shady, the renegade group turns outright criminal, stealing technologies that the SGC fails to negotiate for from other planets, including from Earth's allies the Tollans and the Asgard. Eventually, the rogue NID finally splinters off into the Trust once their wealthy backers are arrested. Freed from any government restrictions, the Trust becomes even more violent, conducting chemical attacks and assassination. When their operatives are driven away from Earth by the SGC, the group manages to get themselves captured and implanted with Goa'uld. Ironically, Ba'al and Athena end up in charge of the Trust and head several major corporations.
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 The Men in Black
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Marvel Cinematic Universe:
The second season of Agents of S.H.I.E.L.D. sees the conflict between two remnant S.H.I.E.L.D groups: Coulson's team, (semi-) officially appointed by Nick Fury himself to rebuild the agency in the aftermath of Captain America: The Winter Soldier and the first season's finale, and the "True S.H.I.E.L.D." led by Commander Gonzales, who (kind of hypocritically) sees Coulson's group as this (thanks to a severe case of Fantastic Racism and Well-Intentioned Extremism).
Iron Fist (2017): The Hand has different groups with different philosophies. At first, it seems that Bakuto's faction of the Hand (of which Colleen Wing is a recruiter) is trying to help people by giving orphaned and runaway kids a place to live, in contrast with Madame Gao's faction, which is a drug-smuggling ring, or the faction that Nobu ran in Daredevil (2015), which kidnapped people for experimentation. Then it turns out that Bakuto and his people are actually just as bad as the others, actively seeking out people who can function in society as perfect sleeper agents for the Hand.
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Dungeons & Dragons:
The Shadow Circle, from the 2nd Edition supplement The Complete Druid's Handbook, is a secret society of druids within the larger druidic order. It sees Nature as a hostile, cleansing force that ensures the survival of the fittest and thinks that civilization has weakened humanity and the demihuman races. They support barbarians and think that people should go back to nature. They use evil and vicious tactics to carry out their beliefs.
The Order of the Emerald Claw in Eberron are an outcast Karrnathi military order who actually serve Erandis d'Vol, leader of the Blood of Vol. Most of them do, admittedly, believe they serve Karrnath, but they're functionally independent at this point and the Karrnathi government has declared them traitors in a very genuine, non-Xanatos Gambit sort of way.
The 3rd Edition Monster Manual V introduced the mind flayers of Thoon. Normal illithids are evil yet rational beings who lurk in the shadows, maniplating other races while taking prisoners as thralls or food. But the mind flayers of Thoon went exploring the outer reaches of the Astral Plane, wound up in the Far Realm, and encountered something called Thoon that gave them an obsession with collecting "quintessence," which they use to power a variety of odd bio-mechanical constructs. None of the "visions from Thoon" that those mind flayers follow display any sort of long-term purpose, and when questioned about it, those illithids will only say "Thoon is Thoon and Thoon is all!"
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Fallout 3 has a benevolent example in the DC chapter of the Brotherhood of Steel, which has more or less gone rogue from the western chapters and abandoned the goal of finding tech at all costs to trying to protect the locals from super mutants and raiders (and eventually the Enclave). However, after the death of the Lyons and Arthur Maxson taking the helm of Elder, the DC chapter eventually reunited with the west coast chapter and refocused their efforts on preserving tech and eradicating mutants and non-humans as of Fallout 4.
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The Black Hand, led by Anton Slavik, go renegade when Hassan (Nod's leader and GDI puppet) tries to execute Slavik. Slavik manages to reconquer the Brotherhood before Kane shows up.
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 Command & Conquer: Tiberian Sun (Video Game)
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Stargate SG-1:
The rogue NID is this for Earth. While the regular NID is rather shady, the renegade group turns outright criminal, stealing technologies that the SGC fails to negotiate for from other planets, including from Earth's allies the Tollans and the Asgard. Eventually, the rogue NID finally splinters off into the Trust once their wealthy backers are arrested. Freed from any government restrictions, the Trust becomes even more violent, conducting chemical attacks and assassination. When their operatives are driven away from Earth by the SGC, the group manages to get themselves captured and implanted with Goa'uld. Ironically, Ba'al and Athena end up in charge of the Trust and head several major corporations.
In one second-season episode, the SGC encounters a species of aliens called the Reetou who exist out-of-phase from the rest of the universe (read: they're invisible) and were mostly exterminated by the Goa'uld because proximity gives the snakes headaches. One faction of Reetou decided to exterminate the Goa'uld, and that the best way to do it was a scorched-Earth (pardon the pun) policy against humanity, whom the Goa'uld use as hosts. The Reetou Central Authority found this reprehensible and sent an agent to Earth to warn the SGC.
Good/evil-flipped with the Ancients, a splinter group from their progenitor race the Ori; the Ancients believe that Sufficiently Advanced Aliens should not play God, whereas the Ori believe that they should, having learned to draw power from mortals' worship of them.
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The True Way Alliance serves as a justification for having Cardassian and Jem'Hadar enemies in the game without conflicting with the ending of Deep Space Nine, in which the Dominion and Cardassian Union made peace with the Federation, Klingons, and Romulans and the Cardassians acquired a civilian-ruled government. The True Way are terrorists who want to restore the old military regime and resume the Dominion War.
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 Star Trek: Deep Space Nine
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Iron Fist (2017): The Hand has different groups with different philosophies. At first, it seems that Bakuto's faction of the Hand (of which Colleen Wing is a recruiter) is trying to help people by giving orphaned and runaway kids a place to live, in contrast with Madame Gao's faction, which is a drug-smuggling ring, or the faction that Nobu ran in Daredevil (2015), which kidnapped people for experimentation. Then it turns out that Bakuto and his people are actually just as bad as the others, actively seeking out people who can function in society as perfect sleeper agents for the Hand.
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Mass Effect 2 reveals that the geth you spent most of the first game fighting are in fact a splinter faction considered heretics by the mainstream geth population, who call themselves the True Geth. The True Geth believe that they and all other creatures should be free to choose their own fates, whereas the heretics serve and obey the Reapers.
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Delta Green:
Once working for the government, the eponymous Delta Green illegally continues its operations to defend America from the Cthulhu Mythos. Unsurprisingly, they also subvert the usual evil nature of the trope, even though they are often quite ruthless — understandably, considering the alternative.
After 2001, Delta Green was reactivated under the pretense of fighting terrorism. Some old members of Delta Green weren't very happy with this and decided to keep the old conspiracy running. The "official" Delta Green is called "The Program" and the "renegade" is called "The Outlaws".
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Mass Effect:
The human supremacist terrorist organization Cerberus started out as the black-ops division of the Human Systems Alliance.
Mass Effect 2 reveals that the geth you spent most of the first game fighting are in fact a splinter faction considered heretics by the mainstream geth population, who call themselves the True Geth. The True Geth believe that they and all other creatures should be free to choose their own fates, whereas the heretics serve and obey the Reapers.
Mass Effect: Andromeda:
The primary example is the Roekaar, who split off from the mainstream Angara Resistance when the Andromeda Initiative arrived in the Heleus Cluster. Rather than just wanting the kett kicked out of Heleus, the Roekaar also want to wipe out the Milky Way colonists and will sometimes murder other angara for "collaborating" with the Nexus or the Exiles. They play a big role in your angara party member Jaal's loyalty mission, which may end in their leader Akksul being discredited before his own followers and the Roekaar mostly disbanding.
The Exiles themselves are an example, being individuals who were banished from the Nexus for various crimes (mainly a mutiny that occurred before Ark Hyperion arrived) and have become Space Pirates to survive. Ryder can work to promote reconciliation over the course of the story.
The krogan broke off into a third faction after they helped put down the mutiny and the Nexus leadership refused to honor the terms agreed to.
The kett in Heleus turn out to be a splinter faction of the main kett empire since the Archon has effectively cut off communication with the kett home world in order to set himself up as de facto ruler of the cluster.
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Rebuild World: In the Private Military Contractors company Drankam, Katsuya's Battle Harem (led by Airi and excepting Yumina) form one of these, disappearing all at once and planning to get revenge on Akira for killing Katsuya and much of the harem, even though it was in self-defence.
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Grand Theft Auto IV: The Lost and Damned has Brian Jeremy start his own splinter faction of the Lost M.C., leading to a Civil War within the gang.
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Destiny 2 has introduced a ton of these over the years to keep the story going.
The Fallen: A species of marauding Space Pirates with a vendetta against humanity, and a Dying Race driven to increasing extremes to survive. Currently divided into:
The House of Dusk: An inversion. The House of Dusk was created when the various rival factions of Fallen from the first game consolidated, pooling their resources for survival.
The Spider's syndicate: The Spider is a Fallen mob boss driven by greed rather than hate, so his relationship with humanity has alternated between benefactor, reluctant ally, and antagonist depending on what kind of profit he stands to make from the situation.
The Scorn: A Zombie Apocalypse of undead Fallen in thrall to the Witness. A threat to everyone in the solar system.
Kell's Scourge: A rival crime syndicate to the Spider's, led by his brother Siviks. Unlike the Spider, he still wanted humanity exterminated and snuck a nuclear-armed Humongous Mecha into the Last City to accomplish this. He and his syndicate were soundly defeated, and the remnants absorbed by the House of Salvation.
The House of Salvation: Splintered off from the House of Dusk, a Rising Empire of well-organized and heavily-armed Fallen led by the warlord Eramis, who has come to despise not just humanity but also the Traveler, which most Fallen still revere. They've since been co-opted by the Witness, who is transforming them en masse into Scorn.
The House of Light: A small group of Fallen who seek peace with humanity, led by the open-minded, Traveler-worshiping Mithrax. Their resources are limited, but they've become steadfast allies.
The Cabal: A militaristic empire. Their attempt to conquer the solar system was defeated in the base game, and their leader Dominus Ghaul slain, but plenty of remnants stuck around to continue fighting. Splinter factions include:
The Loyalists: A rogue faction of the Cabal loyal to the exiled Emperor Calus over the usurper Ghaul. Initially suggested to be potential allies, it eventually became clear Calus's depravity and god complex would do humanity no favors if he was allowed to exert any influence on the Last City.
The Imperial Cabal: Technically the opposite of a splinter faction, being the remnants of the actual Cabal empire now that the Hive have overrun it. Led by Empress Caiatl, Calus's daughter and sworn enemy, they fled to the solar system where, after some initial conflict, they became another of humanity's allies in the name of mutual survival.
Defectors and deserters: Assorted bands of Cabal who oppose Caiatl's leadership for various reasons and ditched the empire, some joining the Loyalists, others becoming independent. Used to handwave the existence of Cabal enemies now that we're buddies with their empire.
The Shadow Legion: A splinter or evolution of the Loyalists, being a brand new army granted to Calus after he allied himself with the Witness for greater power.
The Hive: A Horde of Alien Locusts who serve the Witness directly, obeying a Religion of Evil that demands the Traveler be destroyed and all other sentient life in the universe exterminated.
Grasp of Nokris: A rogue faction led by Nokris, a son of Oryx, one of the species' three gods and progenitors, alongside the renegade worm god Xol. Nokris was disowned and unpersoned after learning necromancy, a heretical form of magic, while Xol fled the other worm gods fearing they would kill it. Together they tried to conquer Mars. Xol was dealt with, Nokris was killed after joining up with Savathûn, and the Grasp of Nokris vanished after Mars itself was collapsed into a singularity by the Witness.
The Lucent Hive: A rogue faction led by Savathûn, the Witch-Queen, one of the species' three gods and progenitors. Savathun became a heretic to her Religion of Evil by embracing the Traveler and its Light, turning against the Witness in the process — but this didn't make her any less of a threat to humanity.
The Vex: A robotic Hive Mind that seeks to infect and convert the universe into more Vex.
The Sol Divisive: A branch of the Vex based in the Black Garden that began worshiping the Darkness (a force tied intimately to the Witness) after they discovered doing so granted them power, which turned them a little strange. The rest of the Vex collective is wary of them, which is said to escalate sometimes into outright violence. As the Vex are a Hive Mind, this says something about how deeply corrupted the Sol Divisive are.
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In Frontier Magic, the mainstream Rationalists simply believe that not being dependent on magic is a good idea; but an isolated settlement of fanatical Rationalists ends up condemning magic as evil.
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Fallout:
Fallout 3 has a benevolent example in the DC chapter of the Brotherhood of Steel, which has more or less gone rogue from the western chapters and abandoned the goal of finding tech at all costs to trying to protect the locals from super mutants and raiders (and eventually the Enclave). However, after the death of the Lyons and Arthur Maxson taking the helm of Elder, the DC chapter eventually reunited with the west coast chapter and refocused their efforts on preserving tech and eradicating mutants and non-humans as of Fallout 4.
There's also the Midwestern Brotherhood in the semi-canonical Fallout Tactics: Brotherhood of Steel. Unlike the main Brotherhood, they have been forced to recruit all-comers from the surrounding areas, eventually even including intelligent Deathclaws, due to many of them dying, when their airships crashed and all contact with the Main Brotherhood was lost. While they're less benevolent than the DC Brotherhood, they are still forced to become protectors of the surrounding area in order to maintain their flow of new recruits and to fight the Calculator's Mecha-Mooks. Of course, the whole reason they were sent out in airships in the first place was that they were already a dissenting faction, claiming that the Brotherhood should extend its mandate to protecting people and open up its membership.
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Mobile Suit Gundam SEED has two major samples:
Blue Cosmos, an anti-Coordinator terrorist group and movement within the Earth Alliance. Many in the Alliance don't share such extremist views. Sadly, Blue Cosmos ends up gaining enough influence to control the policies of the government.
Originally the Moderates within ZAFT, the Clyne Faction break off when the Zala extremists come to power. In a subversion, they're outright good guys. The Faction manage to form an underground resistance, steal key equipment, and join up with the heroes.
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Mobile Suit Gundam Wing:
A splinter group of OZ/the Romafeller Foundation, the Treize Faction opposes the introduction of automated mecha. In an inversion of the trope, the splintering has made Foundation come off as increasingly villainous, though Treize is hardly a saint himself.
In Mobile Suit Gundam Wing: Endless Waltz, it's revealed that the Gundam pilots have split from the Barton Foundation. Disagreeing over the goal of world conquest, the pilots decide to focus on stopping OZ instead.
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Star Trek:
The main bad guys in Star Trek: Bridge Commander are a rogue Cardassian faction who have found a powerful new race and are tricking them into building the faction powerful ships, as well as the technology to make stars go boom.
Star Trek Online:
The True Way Alliance serves as a justification for having Cardassian and Jem'Hadar enemies in the game without conflicting with the ending of Deep Space Nine, in which the Dominion and Cardassian Union made peace with the Federation, Klingons, and Romulans and the Cardassians acquired a civilian-ruled government. The True Way are terrorists who want to restore the old military regime and resume the Dominion War.
Inverted with the Romulan Republic, the faction for Romulan player characters. They broke away from the Romulan Star Empire after the Hobus supernova and Empress Sela and the Tal Shiar seizing control and are a democratic polity that just wants to rebuild Romulan society in peace.
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The main villains of Time Crisis 4, the Bio-Weapons Special Ops Unit (often referred to as the Hamelin Battalion), are revealed to be this to the U.S. Army.
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The Chaos Space Marine Legions split off from the Imperium during the Horus Heresy because Horus was tricked into believing that the Emperor would make himself be worshiped as a god and betray half his Primarchs. The Horus Heresy caused that to happen. It's also heavily implied that the Blood Ravens are a splinter chapter from the Thousand Sons Legion, one of the ones that went rogue. The Black Legion has the 3 warbands collectively known as the Thrice Cursed Traitors who refuse Abaddon the Despoiler's leadership.
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A Man of Iron: One of the main antagonists in A Crack of Thunder is Ivan Vanko, who along with Asha Greyjoy is leading a group of Ironborn on a Roaring Rampage of Revenge against the lords of mainland Westeros. However, it's eventually revealed that this is being done without Balon Greyjoy's consent; he's so pissed by the defiance to his will (and how it ruins his own plans for launching a war) that he commands all Ironborn back to Pyke to reaffirm his control over them.
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In Galactic Civilizations II, mirroring (and probably a deliberate Shout-Out to) the Star Control example, the Korath Clan, which believes that other races should be exterminated outright, rebels against the villainous Drengin Empire.
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In Girl Genius, Madwa Korel's faction of Smoke Knights chose (or were possibly brainwashed into) loyalty to the Other, subsequently all other factions of Smoke Knights will drop their current missions and conflicts with each other to take out Madwa or any of her Knights should they encounter them.
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Gundam has a variety of examples:
Mobile Suit Gundam SEED has two major samples:
Blue Cosmos, an anti-Coordinator terrorist group and movement within the Earth Alliance. Many in the Alliance don't share such extremist views. Sadly, Blue Cosmos ends up gaining enough influence to control the policies of the government.
Originally the Moderates within ZAFT, the Clyne Faction break off when the Zala extremists come to power. In a subversion, they're outright good guys. The Faction manage to form an underground resistance, steal key equipment, and join up with the heroes.
Mobile Suit Gundam Wing:
A splinter group of OZ/the Romafeller Foundation, the Treize Faction opposes the introduction of automated mecha. In an inversion of the trope, the splintering has made Foundation come off as increasingly villainous, though Treize is hardly a saint himself.
In Mobile Suit Gundam Wing: Endless Waltz, it's revealed that the Gundam pilots have split from the Barton Foundation. Disagreeing over the goal of world conquest, the pilots decide to focus on stopping OZ instead.
Mobile Suit Gundam 00 provides several examples:
La Eden, a violent right-wing political group within the AEU (though not supported by the superpower), commits a series of terror attacks to stop the protagonists. Celestial Being responds by simultaneously curb-stomping the entire faction.
Team Trinity claims to be part of Celestial Being, sharing the similar technology and goal of eliminating warfare. However, the Trinities are much more ruthless, attacking without provocation or mercy. Eventually, the two groups come into conflict.
The Innovators are originally part of Celestial Being, but thanks to the events of Season 1, the two groups splinter, with the Innovators causing most of the problems for the next season.
Splintering off from the Federation military, the ESF Coup detat Faction seeks to expose the A-Laws' atrocities. Like the Trieze Faction, their going "renegade" makes the Earth Sphere Federation come off as increasingly antagonistic.
Mobile Suit Zeta Gundam: Though officially part of the Earth Federation serving as a special security force, the Titans are used by a corrupt politician to gain control of the Earth Sphere. Their actions are zealous, including gassing an entire colony. Eventually, they go full renegade after they're exposed by the AEUG.
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An episode of NCIS features a group called the "MAH" (Military at Home), who believe that America should focus on fighting crime and social problems, instead of policing the world. A group of MAH decides to take it a step further, plotting to destroy a communications tower to make a point, with no intention of harming anyone. However, the renegade group also has a splinter group who decide to attack people as well.
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The sinister Beylin Fist faction in Metal Fight Beyblade have splintered from China's Beylin Temple training school.
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In Wings of Fire the LeafWings are divided into the "original" group, referred to as SapWings, and the PoisonWings, who split off due to being more hardliners about taking revenge on and killing the HiveWings.
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Hunters of Justice: The Red Fang is a group of extremist former White Fang members who refuse to give up their hatred of humans in the face of Braniac's invasion. Led by Adam Tarus, the Red Fang kill or mutilate humans and Faunus they deem "traitors" in the bottled Kingdom of Vale.
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Infinity Crisis: A recurring threat throughout the spinoffs/sequels is a rogue faction of warmongering Skrulls opposed to Talos' peaceful leadership, who want to return their people to the days of conquest. To this end, they've started infiltrating other universes to subvert those worlds' resources to their own aims.
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Hand of Thrawn features a power struggle between Pellaeon and a group of Imperial officers led by Moff Disra that seeks to derail his efforts to negotiate peace with the New Republic, nearly managing to start a civil war in the New Republic in the process.
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BattleTech:
The Word of Blake is a conservative faction of ComStar which broke off when the mother organization reformed to lessen focus on its mystical aspects. The Word eventually started an all-out war that affected in entire Inner Sphere.
On the Clan side, the Society is (or was, the Clans certainly did their best to stamp them out upon discovering their existence) this to the scientist caste at large, believing in their own group's superiority over the ruling warrior caste and secretly working towards an eventual goal of supplanting the latter at the top. The Wars of Reaving forced their hand well before they were truly ready.
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In Command & Conquer: Red Alert, it's a staple to include at least one mission where the Soviets fight against each other. In the third game, the Allies get some of this too, led by the President of the United States to boot.
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Halo: Escalation: Sali 'Nyon decides to break off from Jul 'Mdama's anti-human and Forerunner-worshipping Covenant remnant and start his own, all because Jul destroyed the Forerunner world of Requiem and has the human Dr. Halsey working for him.
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There's also the Xenos Hybris, who spurn the Fantastic Racism against xenos the Imperium enforces and believe humanity should seek peaceful relations and even alliances with alien races and facilitate cultural exchange, usually on the fringes of the Imperium where the dogmatic laws of the Imperium that forbid this can't be enforced effectively. They also frequently smuggle in Xenos tech (seen as heretical in the Imperium) to study. Of course, depending on the xenos in question, this isn't necessarily "evil" outside the Imperium's xenophobia.
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Command & Conquer:
In the Command & Conquer: Tiberian Series, the Brotherhood of Nod has a chronic issue with these. Various factions of the Brotherhood end up fighting with each other for power; Kane is the only one to really unite them all. Here are a few notable examples:
The Black Hand, led by Anton Slavik, go renegade when Hassan (Nod's leader and GDI puppet) tries to execute Slavik. Slavik manages to reconquer the Brotherhood before Kane shows up.
CABAL, after manipulating both sides to accomplish its goals, is so much of a threat that both GDI and NOD work together to eliminate it.
Believing that the Brotherhood strayed from its "pure" path, Marcion took the Black Hand into exile and reformed the group into a religious order, one of the many splinter factions after CABAL's defeat and Slavik's death.
The Nod Separatists oppose Kane's alliance with GDI, seeing it as a betrayal of their own core beliefs.
GDI tends to be a rather stable bunch, but in Tiberian Twilight, one GDI army goes rogue over the alliance with Kane, which leads to infighting within the organization.
In Command & Conquer: Red Alert, it's a staple to include at least one mission where the Soviets fight against each other. In the third game, the Allies get some of this too, led by the President of the United States to boot.
Command & Conquer: Generals:
One mission has a renegade Chinese army (allied with the Middle Eastern Terrorists who are the game's main antagonists) as one of the enemies. In this game, China is one of the "good" factions.
The final U.S. mission in Zero Hour has the player allying with the GLA against Dr. Thrax, whose use of bioweapons disturbs even them. The first GLA missions focused on it reforming by defeating splinter factions led by the likes of Stealth Expert Prince Kassad.
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Forever Home: Downplayed with the Judgment Faction and the nation of Tren, since the latter is still an aggressor towards Auria, but isn't nearly as destructive as the faction. Eventually, this is played straight when Tren makes peace with Auria in order to save the planet from the Judgment Faction.
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One Piece: The antagonists of the movie Film: Z are the Neo-Marines, a group of Marines who went rogue from the regular Navy because they felt that even Fleet Admiral Sakazuki wasn't going far enough to deal with pirates. To rectify what they see as the problem, they intend to destroy the entire Grand Line and then spread out from there to purge all pirates elsewhere, regardless of civilian casualties.
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Starfinder: When the undead-ruled planet Eox joined the Absalom Pact, part of its military broke away to form the anti-living Corpse Fleet.
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In the post-Zero Hour: Crisis in Time! era of Justice League International, Captain Atom decides to form his own Justice League team with others as he believes that the League headed by Wonder Woman isn't the "real" Justice League, leading to the Extreme Justice title. In a subversion, they're still good guys and they still call themselves the Justice League, they just find Diana's clubhouse take to be too silly.
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In Metal Gear Solid, FOXHOUND — originally an advanced special forces unit — goes rogue and takes over a research base holding nuclear weapons and the means to launch them, kidnapping the DARPA Cheif and ArmsTech President. This is especially bad since FOXHOUND would have been the go-to unit to solve this sort of situation if they weren't the ones creating it! Instead, former FOXHOUND operator Solid Snake is asked to save the world by his old friend and former FOXHOUND commander, Colonel Campbell.
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In Terra, the Shadow Cabal started as a personal army for the Sovereign of the Asurian Empire (the founder is Sovereign Northazul Kalar's son Solus), but it mutated into a barely controllable paramilitary faction with its hands in everything from slave-raiding to salvage operations.
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WILLE of Rebuild of Evangelion consists of former NERV agents who oppose the progenitor agency. In an inversion of the trope, WILLE's goals are benevolent compared to NERV's, but their means are just as ruthless.
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Skullgirls lore has the Anti-Skullgirl Labs, who conduct research in order to understand the Skull Heart and develop weapons to destroy the Skullgirl it periodically creates. Unfortunately, they aren't exactly known for the humane treatment of their test subjects. After his wife became a Skullgirl and was subsequently killed, the King had a change of heart and decommissioned the Labs, but later disappeared under mysterious circumstances. Several members of the ASG Labs took advantage of this and moved to restart the experiments, this time without official supervision and with even shadier laboratory practices. Finally, one sect, Lab Zero, broke off entirely, operating in complete secrecy even from the other rogue Labs — their methods are also much, much more heinous than the others. It's implied that the restarted Labs may have reformed to be more ethical after Princess Parasoul came into power, making the situation a (partially, at least) subverted example of the trope.
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In Star Trek Into Darkness, Starfleet's Section 31 has its own agenda.
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Blown Away takes great pains to emphasize that the villain was definitely not in the IRA because he was "too crazy for them". (Oddly, the film is less reticent about claiming that he did freelance work for the Red Brigades and the Libyan government. This was possibly due to the IRA being more popular with Americans than the others.)
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Legends of Baldur's Gate: A splinter of the Cult of the Dragon (part of the Forgotten Realms source material) is the main antagonist. Unlike the original, the splinter believes in usurping the power of evil dragons rather than just worshipping them.
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The Godzilla vs. Kong novelization states that Monarch suspect the Titan poachers in Godzilla: Dominion and the novel's prologue, who tried to capture Na Kika before Godzilla destroyed their oil rig, might have been a rogue splinter group from the eco-terrorists who featured in Godzilla: King of the Monsters (2019) — this theory is one of the many things that Mark Russell is sceptical of in the book. The poachers' interest in exploiting the Titan's biological materials for profit in the novel's prologue is similar to how the eco-terrorists fund their operations by trafficking Titan DNA, but unlike them, the poachers are entirely self-serving and have no higher end-goals beyond making themselves a good buck.
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Bait and Switch (STO): Reality Is Fluid reveals that the Undine responsible for the attacks on the Federation and Klingon Empire in Star Trek Online are members of a rogue tribe. Kanril Eleya makes peaceful contact with another tribe that considers them "shameful" and "beneath contempt", and defeats them offscreen; these Undine subsequently aid The Alliance during the Iconian War in Beat the Drums of War.
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Warhammer 40,000:
The Chaos Space Marine Legions split off from the Imperium during the Horus Heresy because Horus was tricked into believing that the Emperor would make himself be worshiped as a god and betray half his Primarchs. The Horus Heresy caused that to happen. It's also heavily implied that the Blood Ravens are a splinter chapter from the Thousand Sons Legion, one of the ones that went rogue. The Black Legion has the 3 warbands collectively known as the Thrice Cursed Traitors who refuse Abaddon the Despoiler's leadership.
The Farsight Enclave broke away from the Tau Empire out of a dislike for the Ethereal caste's control of the Empire. Commander Farsight still agrees in principle with the aims of the Empire; the sticking point is the means. It may be an inversion since both the Farsight Enclaves and the Tau Empire have dark secrets.
The Inquisition is divided into many political subfactions, collectively known as Puritan and radical. Some radical groups largely follow Imperial dogma but use more unorthodox methods (that are inherently viewed with suspicion) to fulfill their goals and are accepted as a necessary evil by all but the most extreme Puritan factions. Others fit this trope to a tee, with many being illegal secret societies.
You have the Recongregationists, a group who resents the way the Imperial government has developed and want to abolish and replace the majority of its institutions and greatly restructure the rest. Of course, given that the Imperium is "the bloodiest regime imaginable" that isn't necessarily more evil than the rest of the Inquisition…
Then there's the Istvaanians, named for the Istvaan V Dropsight Massacre in the aforementioned Horus Heresy, who believe that the Imperium thrives off of conflict, using it to grow stronger and more resilient and produce more experienced warriors to defend it, and often deliberately provoke more conflict with enemy factions or, failing that, outright civil war in many regions (which sadly, is already quite common).
There's also the Xenos Hybris, who spurn the Fantastic Racism against xenos the Imperium enforces and believe humanity should seek peaceful relations and even alliances with alien races and facilitate cultural exchange, usually on the fringes of the Imperium where the dogmatic laws of the Imperium that forbid this can't be enforced effectively. They also frequently smuggle in Xenos tech (seen as heretical in the Imperium) to study. Of course, depending on the xenos in question, this isn't necessarily "evil" outside the Imperium's xenophobia.
The most extreme is probably the Xanthites, who believe in using Chaos against itself, and other enemies of the Imperium. Such tactics include creating Daemonhosts to use as elite warriors, summoning and binding demons themselves, using chaos artifacts to enhance their power for combat, and other such methods that would typically get anyone else executed as a heretic, were it not for their position as the people in charge of doing exactly that. Given that Chaos is known to be incredibly difficult to control and also acts as The Corruption, this often backfires. However, there have been times where these tactics proved to be a viable alternative to the usual extremely destructive and costly methods of the Imperium.
The Puritan Thorian sect, who believe that The God-Emperor can be reborn in the flesh have the Horusians, who believe in a syncretic mixture of Chaos Worship and the Imperial faith and believe that the best way to bring back the Emperor is as a Chaos Avatar, seeing Horus as a missed opportunity to do so. Naturally, pretty much everyone, even the Xanthites, think they're completely insane.
The Xanthites and the Recongregationists have their own, even more radical splinter sects who are by and large officially considered traitors. The Recongregationists have the Seculos Attendous, who forgo the God Before Dogma philosophy of the main group for outright antitheism, seeking to destroy the whole Ecclesiarchy (the Imperial Church) and eliminate all faith in the God-Emperor entirelynote Which is, ironically, exactly the position the Emperor himself held.. The Xanthites have the Phaenonites, who wish to destroy both the God-Emperor and the Chaos Gods, and then use the power of the Warp and cybernetics to turn Humanity into a race of godlike beings.
Within the Puritan side, there is the Monodominants, extremists even by the Imperium's standards who even other Inquisitors look up as excessive, indiscriminate and prone to trampling over everyone in their path, and whose zeal has a tendency to leave them blind to things like "the Imperium kinda needs Astropaths and Navigators, so you can't do away with all psykers and mutants".
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Shadowrun: Black Star was a paramilitary offshoot of Anarchist Black Cross that became more mercenary after falling under the sway of a charismatic and possibly corporate-backed leader. They were mostly wiped out in the Az-Am war though.
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Illuminatus!: Morituri are an offshoot of The Weather Underground, whose members are all teenagers. The Cult of the Black Mother is a more secretive, and thus harder to infiltrate, branch of the Black Power movement. The Justified Ancients of Mumu, The League of Dynamic Discord, and the Erisian Liberation Front are all radical offshoots of the Illuminati and each other.
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In Son of the Sannin, a minor subplot deals with Hinata becoming head of the Hyuga Clan after she awakens the Tenseigan, due to the power it entails, and her first official act is to abolish the Caged Bird Seal practice altogether to eliminate the division of Main and Branch houses. Naturally, this causes a serious stir as many members do not conform to this, and the Hanabi Gaiden sidestory reveals that they even planned to split and form their own clan until they were killed by Hanabi while plotting to murder her along with Hinata and their mother.
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Eclipse Phase:
Project OZMA, the Planetary Consortium's secret agency, might be only pretending to being loyal to PC and long since became a pseudo-Illuminati-like organization.
The alliance of Minervan Fleet and Special Intelligence Secretariat. The former is a Jovian deserter fleet of military men who wanted a more proactive and permanent policy against transhumanity, while the latter are former Jovian Space Force Intelligence personnel who lost the power struggle in Jovian politics. Both of them see themselves as the true Jovian government.
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Perfect Dark: The director of the NSA, Trent Easton, is in league with a shadowy conspiracy — and unlike today's NSA, Easton seems to have his own personal army. In order to accomplish their goals, Easton plans to replace the President with a clone as part of a larger scheme.
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Doctor Who:
The villainous Ice Warriors led by Azaxyr in "The Monster of Peladon" are said to be an extremist group who want to revive their culture's aggressive warrior tradition, since the previous Ice Warrior story had established them in general as having become good galactic citizens.
The, ahem, Renegade and Imperial Daleks who battle it out in "Remembrance of the Daleks", though the so-called Renegades are actually the mainstream Daleks, while the Imperials are a new species of Daleks created by Davros and conditioned to be loyal to him personally. They both view each other as offences against genetic purity, though.
"The Time of the Doctor" reveals that Madame Kovarian and the Silence who were terrorizing the Doctor during Series 5 and 6 were this. In the episode, we see the events on Trenzalore that caused them to break away from their organization, travel back in time, and attempt to prevent the Doctor from ever reaching the planet in the first place. However, their meddling with the past is what causes the Doctor to travel to Trenzalore in the first place. Plus, the reason why they didn't want the Doctor going to Trenzalore was that if he did, they feared he would release the Time Lords back into reality and the Time War would restart, running the risk of causing equal if not greater devastation as the first time. Their first big plan to stop the Doctor ended up destroying the entire universe.note However, they might have been planning for the Doctor to do what he did to restore it, which would have erased him if not for his Companions holding onto his memory, which allowed the same twisting of reality to restore him, but that is a very dangerous game. Considering that it was indicated that the Time War inflicted catastrophic damage on more than just the basic physical plane of the universe, maybe they considered 'just' the destruction of the universe to be a fair price to pay.
"The Zygon Invasion"/"The Zygon Inversion" is based on the idea that the Zygon refugees who were welcomed onto Earth in "The Day of the Doctor" have spawned a Renegade Splinter Faction who want to conquer Earth.
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In Fire Emblem: The Sacred Stones, Eirika faces such a faction during her route. The nation of Carcino is divided between the Kilmt faction (which wishes to stay allies with Frelia) and the Pablo faction (which is aligned with Grado). Using unscrupulous means, Pablo takes over the country and attempts to hinder Eirika.
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The Majestic 12 from Deus Ex are that part of The Illuminati who shed "ethical inflexibility".
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Ladyhawke: The Bishop of Aquila, who serves as the film's antagonist and is so far gone as to consort with the forces of darkness for vengeance over a romantic infatuation being unreciprocated, is described as "an evil man, a powerful man, hated and feared; rejected even by Rome itself."
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The Crimson Jihad in True Lies is a splinter group that broke off from a larger Islamic terrorist organization (possibly Islamic Jihad), apparently because their leader Salim Abu Aziz didn't think the bigger group was crazy enough.
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The crew of the Darksyde in Beast Wars are considered to be criminals by the larger Predacon faction — not because of any offense to Predacon morality, what little there is to offend, but because their blatant theft of Maximal artifacts and attack on their personnel incur reprisals that are a serious hindrance to the more subtle long-term plans of the Predacons as a whole. That and Megatron's ambition and sheer ruthlessness make even them a little nervous.
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Andromeda has the Knights of Genetic Purity, who utilize highly advanced technology to hunt down and eliminate any genetically engineered humans, particularly Nietzscheans, whom they blame (rightly) for the fall of the Commonwealth. While they're too weak to take on the major Nietzschean prides like the Drago-Kazov and the Sabra-Jaguar, they have no problems with going after the lesser ones. Then it's revealed that the Genites (as they're known) are a splinter group of the Templars, founded by Admiral Constanza Stark, Dylan's former superior. While the Templars mainly focus on secretly helping rebuild the Commonwealth, they also plan to destroy the Nietzscheans. The Genites simply take it one step further and go after all genetically engineered people, which represent the vast majority of humans at this point (Dylan himself is half-Heavyworlder). It's also clear that the Genites are much better equipped than their parent organization.
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In the Command & Conquer: Tiberian Series, the Brotherhood of Nod has a chronic issue with these. Various factions of the Brotherhood end up fighting with each other for power; Kane is the only one to really unite them all. Here are a few notable examples:
The Black Hand, led by Anton Slavik, go renegade when Hassan (Nod's leader and GDI puppet) tries to execute Slavik. Slavik manages to reconquer the Brotherhood before Kane shows up.
CABAL, after manipulating both sides to accomplish its goals, is so much of a threat that both GDI and NOD work together to eliminate it.
Believing that the Brotherhood strayed from its "pure" path, Marcion took the Black Hand into exile and reformed the group into a religious order, one of the many splinter factions after CABAL's defeat and Slavik's death.
The Nod Separatists oppose Kane's alliance with GDI, seeing it as a betrayal of their own core beliefs.
GDI tends to be a rather stable bunch, but in Tiberian Twilight, one GDI army goes rogue over the alliance with Kane, which leads to infighting within the organization.
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Given that the Klingons are Cold War analogs, the renegade Klingon commander on Star Trek V: The Final Frontier counts as a sci-fi version of this trope.
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Xcom 2: An unusual example since both organizations are still on good terms, but XCOM has one in the form of The Templars, who were formed out of the survivors of their Psionics Division, who were developing Psi Operatives at the time. When XCOM was defeated by the invaders, they no longer had any leadership to guide them. Geist, the first agent to successfully develop Psionics, took charge of the group, turning it into a secretive religious order dedicated to honing members' latent psionic abilities and using them to oppose ADVENT. After Bradford managed to unite various survivors of the original XCOM and Earth's militaries into The Remnant to continue the fight against ADVENT, the two organizations reestablished contact and joined forces, but like the other resistance groups, remain an independent partner rather than rejoining XCOM proper.
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Doctor Who (Titan) introduced the Volatix Cabal, who are a Renegade Splinter Faction of the Time War era Daleks and manage to achieve the almost impossible and be even worse than them (they're an entire culture of Ax-Crazy sadistic Mad Doctors).
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The final season of Codename: Kids Next Door hints at a splinter cell of KND agents who want to remove all adults, good or bad, from the world. However, "Operation: T.R.E.A.T.Y." reveals that the cell doesn't really exist, and it's actually a cover for a different organization, revealed in the Grand Finale as the Galactic Kids Next Door.note They're extremists because they've discovered something is wrong with the universe — some alien civilizations have dozens of parents for one kid, with all the horrible implications, and it's spreading. In a way, the KND seen throughout the show is the renegade splinter faction, having been founded based on a time capsule from the Galactic KND but desiring coexistence between kids and parents.
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One sidequest in Beyond Skyrim deals with a small breakaway group from the main game's secessionist Stormcloak faction tentatively called "the Stormcloak Breakaways". Like the main Stormcloak army, the Breakaways want to see Skyrim made independent from The Empire, but while their progenitors only aim to drive the Imperials out of Skyrim and remove Imperial-aligned leaders from power, and are at least pragmatic enough to realize that escalating the conflict to an all-out war with Cyrodiil would be a bad idea, the Breakaways believe that the only way to liberate their country is to kill the Empire itself, and planned to infiltrate Cyrodiil attack the Imperial City directly.
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Ben 10: Omniverse: The Rooters started out as the black-ops division of the Plumbers but split off to begin their own agenda: to free the universe of Ben Tennyson. However, they aren't technically renegades until the end of their story arc, in which their Plumber status is revoked.
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Star Wars Paranormalities Trilogy: The Seferite Order are an inversion, being a more benevolent splinter faction of the Valkoran Empire that performed a Heel–Face Turn following Emperor Valkor's decision to exterminate all life on Christophsis just to torture Zolph Vaelor with Force backlash. The Seferites still desire to carry out their parent faction's claim of trying to make the galaxy more stable (especially in the wake of the Yuuzhan Vong war), but without the desire for galactic conquest and being another cult for the Forceless Collective. What's left of the Valkoran Empire after the Seferites' formation are a group of unhinged fanatics that have doubled down on their loyalty to the Collective.
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Travelers: The main characters are time travelers who came to our time to prevent their Bad Future, mainly by averting catastrophic events. Later there arises another group, calling themselves simply The Faction, who believes that the real problem is overpopulation, and thus the solution is mass murder.
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What It Takes: Athena and her followers are treated like this after Nanda Parbat is nuked. As far as everyone else is concerned, that is the end of the true League of Assassins, and they're just a band of sycophants uselessly holding on to a bunch of outdated traditions that don't even matter anymore. When they become too much of a nuisance, the heroes decide to set Talia on them, not even bothering to deal with them themselves.
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The Legend of Korra:
Originally splitting off due to the White Lotus' decision to become a public organization that openly helps the Avatar, the Red Lotus is instead a group of Anarcho-Primitivists who seek the dissolution of all government and authority, along with the Avatar's destruction.
Kuvira's army started out as one to Zaofu's security force, hurrying off to restore order to the Earth Kingdom due to Kuvira seeing Su's hesitation as cowardice. Kuvira becomes powerful and popular enough that when she ousts the current Earth Kingdom heir, she is greeted with applause.
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In Pokémon Reset Bloodlines, it's revealed that Maxie and Archie used to be part of a bigger organization known as Team Zenith in their bid to change the world (and even worked together for a while), but due to disagreements and infighting ultimately decided to take each his own path and founded Teams Magma and Aqua respectively.
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GDI tends to be a rather stable bunch, but in Tiberian Twilight, one GDI army goes rogue over the alliance with Kane, which leads to infighting within the organization.
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In Digimon Tamers, the protagonists believe that since the Devas are serving one Digimon Sovereign, all four might be against them. It turns out that Zhuqiaomon, the Sovereign who the Devas serve, is acting on his own. He and the other three leading Digimon couldn't agree on a single defense strategy against the D-Reaper.
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Stargate Atlantis:
After Michael is rejected by his fellow Wraith for being a Half-Human Hybrid, he goes off on his own and forcibly turns a large group of humans into hybrids like him, while also modifying himself so that he doesn't need to feed on humans anymore (freeing himself from this weakness). His goal is to destroy both the humans and the Wraith, establishing the hybrids as the dominant race in the Pegasus Galaxy. In a Bad Future, he succeeds.
Atlantis also introduces the Vanir, a rogue group of Asgard, who believe that their species must survive at any cost, up to and including experimenting on humans to solve their Clone Degeneration problem. Millennia ago, they split off from the larger Asgard group and left for the Pegasus Galaxy, where they started experimenting on humans without any oversight. In modern times, they are perfectly willing to cause untold destruction across the galaxy in order to keep the Wraith contained. When they find out that their Asgard cousins have all died out, it only serves as proof to them that they were right all along.
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Star Wars Legends: This is frequently an Enforced Trope used to retroactively fix various Continuity Snarls.
The Jedi Order went through its share of schisms even outside of the various Sith Wars, with the mainstream Jedi Council often considering the schismatics to be heretics even if they were still light-sided.
For millennia, the Corellian system had its own indigenous Jedi sect, the Green Jedi, which maintained an independent Jedi Council.
The Republic Commando Series retconned the roving ship-based Jedi academy Chu'unthor, where Callista Ming trained, as being run by a renegade Jedi Master named Djinn Altis. In particular, Altis refused to abide by the Jedi Order's ban on romantic relationships.
Coruscant Nights has a secondary character, Laranth Tarak, who before the Jedi Purge was a member of the Gray Paladins, a Jedi sect considered heretical by the Jedi Council mainly for preferring blasters to lightsabers.
The Glove of Darth Vader:
The Empire is presented as being headed by the Central Committee of Grand Moffs, with Trioculous as a Puppet King and the Prophets of the Dark Side being the ones really pulling the strings. While this series was poorly received and mostly rendered Canon Discontinuity, later supplemental material shoehorned it back into continuity with some handwaving, the most prominent case being that this Imperial faction was actually a splinter that broke away from the central government on Coruscant, which was at the time under the control of Ysanne Isard and her pawns on the Imperial Ruling Council according to the X-Wing Series.
The aforementioned Prophets of the Dark Side are actually this twice over, as the same supplemental materials that retconned the Central Committee as a splinter faction reveal that they're not the real Prophets (which are a legitimate Dark Side cult recruited by Palpatine) but a bunch of fraudulent imposters established by Imperial Intelligence to act as a Propaganda Machine, only to eventually go rogue by means of setting up the Committee as their puppets to take over the Empire for themselves. Since Isard is Director of Imperial Intelligence, this means they're not just defying her pawns but her directly.
Quite a few warlords and splinter factions (to the point that Wookiepedia has an entire category page for them all) break away from the Empire as it falls apart over the years, for a variety of reasons, and regularly fight the New Republic, the "regular" Empire, and each other from approximately the X-Wing Series to The Callista Trilogy. In Darksaber, Admirals Daala and Pellaeon assassinate most of the leaders of these factions to reunite the Imperial Remnant under one banner.
Hand of Thrawn features a power struggle between Pellaeon and a group of Imperial officers led by Moff Disra that seeks to derail his efforts to negotiate peace with the New Republic, nearly managing to start a civil war in the New Republic in the process.
The Second Imperium from the Young Jedi Knights was retconned to be one of these because the later-published but chronologically-earlier Hand of Thrawn duology established that Pellaeon had successfully established peace between the main Imperial Remnant and the New Republic several years before Young Jedi Knights takes place.
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The New Order Last Days Of Europe: The SS, led by Heinrich Himmler, has mostly split off from the greater Reich, as Himmler has found them too decadent for his tastes and decided to engineer a new form of government to correct this: the Burgundian System, named after his Burgundy territory. Anyone championing it is inevitably a renegade from regular old National Socialism, championing for a system where even the Master Race is treated like ill-fed conscripts at best because The Spartan Way is the only way. The less said about everyone else, the better.
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In Star Control II, the victorious Ur-Quan conquerors are split in a Doctrinal War between the Kzer-Za, a faction that believes that their enemies should simply be enslaved as Battle Thralls, and the Kohr-Ah, which believes they should be annihilated. Unlike the average version of this trope, the split happened long before the Ur-Quan (Kzer-Za) invasion of Free Alliance space — it just wasn't relevant prior as the two deliberately went off in different directions and wasn't to meet again until the time of Star Control II to see who the superior force was. The Reveal of this trope also shows that the war between the Kzer-Za and the Free Alliance, while ending in the victory of the former, has severely depleted their strength, which may spell their defeat in the Doctrinal War, meaning the Kzer-Za would stand back and allow their Kohr-Ah cousins to wipe out every other race in the galaxy. Nice Job Breaking It, Hero.
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The Republic Commando Series retconned the roving ship-based Jedi academy Chu'unthor, where Callista Ming trained, as being run by a renegade Jedi Master named Djinn Altis. In particular, Altis refused to abide by the Jedi Order's ban on romantic relationships.
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Code Prime:
Halfway through R2, Starscream and Schneizel manage to temporarily seize control of the Decepticon regime thanks to their surprise attack with Damocles. Said attack wipes out almost half of the Autobots and Black Knights, and seemingly succeeds in killing Megatron. With most of their enemies eliminated, the rogue faction — composed of Starscream, Schneizel, the Constructicons, and the few members of the Britannian Royal family that were not killed or defected to the heroes side — plans to bombard Earth with the station's cannons and then re-establish the Britannian Empire off-world as a Decepticon vassal state. Their reign is short-lived, however, with Megatron (who stole V.V.'s Code and is thus now immortal) returning, alongside the Predacon, and with help from Slipstream, Thundercracker and Sky-Byte (who all got tired of Starscream's jackass attitude) infiltrate the Damocles, kill all the rebels and take control of the station for themselves.
Later on, Thundercracker, Slipstream and Sky-Byte, along with Steeljaw, break off from Megatron in moral outrage when they learn the full extent of Neo-Ragnarok.
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Mass Effect: Andromeda:
The primary example is the Roekaar, who split off from the mainstream Angara Resistance when the Andromeda Initiative arrived in the Heleus Cluster. Rather than just wanting the kett kicked out of Heleus, the Roekaar also want to wipe out the Milky Way colonists and will sometimes murder other angara for "collaborating" with the Nexus or the Exiles. They play a big role in your angara party member Jaal's loyalty mission, which may end in their leader Akksul being discredited before his own followers and the Roekaar mostly disbanding.
The Exiles themselves are an example, being individuals who were banished from the Nexus for various crimes (mainly a mutiny that occurred before Ark Hyperion arrived) and have become Space Pirates to survive. Ryder can work to promote reconciliation over the course of the story.
The krogan broke off into a third faction after they helped put down the mutiny and the Nexus leadership refused to honor the terms agreed to.
The kett in Heleus turn out to be a splinter faction of the main kett empire since the Archon has effectively cut off communication with the kett home world in order to set himself up as de facto ruler of the cluster.
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Street Fighter IV has S.I.N., a splinter faction of Shadaloo that has broken off after Bison's supposed death in Street Fighter II. It was led by Seth until Juri overthrew him and took over the organization.
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Monarch: Legacy of Monsters: In the back half of Season 1, Shaw and Duvall organize a group of likeminded Monarch operatives into going rogue against what they see as the organization's Head-in-the-Sand Management, taking the proactive step of bombing the portals to Hollow Earth in order to keep any more Titans from emerging, but ignoring the fact that doing so risks provoking another attack regardless.
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Star Trek VI: The Undiscovered Country features renegade officers from both the Federation and the Klingon Empire conspiring together to prevent peace talks between their leaders.
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Monstress: The Blood Court is composed (aside from the Lord Doctor's personal cult) of various Arcanic warlords who no longer acknowledge the authority of the Dawn and Dusk Courts and have banded together to restart the war with the Federation on their own terms. And as those warlords control the bulk of the Arcanics' military might, this makes the Blood Court the most powerful faction on the planet.
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Babylon 5:
Home Guard is a xenophobic paramilitary faction within the Earth Alliance, committing attacks on aliens.
The faction of the Minbari Warrior Caste who tried to kill Kosh in "The Gathering".
A different Minbari Warrior Caste extremist group causes some trouble in "Points of Departure" when Sheridan is first appointed commander of Babylon 5.
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Scorponok's group of Decepticons, who refuse to accept peace with the Autobots and go rogue to keep fighting them and organic life.
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Black Cell in Swordfish is an unofficial counter-terrorist unit founded by J. Edgar Hoover to do whatever it takes to protect America. It's the unit Gabriel heads, planning to steal DEA slush money to fund his vigilante activities. Black Cell goes full rogue when the Senator overseeing the unit tries to terminate Gabriel, but the ending implies that they still continue following their original mandate, as a news report mentions the destruction of a yacht belonging to a sheik suspected of funding terrorists.
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The following is a list of statements referring to the current page from other pages.

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Betrayal Tropes
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Organization Index
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Villains
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type
Renegade Splinter Faction
 Advanced Dungeons & Dragons 2nd Edition (Tabletop Game) / int_5ecdd585
type
Renegade Splinter Faction
 Avatar Legends: The Roleplaying Game (Tabletop Game) / int_5ecdd585
type
Renegade Splinter Faction
 Castle Falkenstein (Tabletop Game) / int_5ecdd585
type
Renegade Splinter Faction
 Chronopia (Tabletop Game) / int_5ecdd585
type
Renegade Splinter Faction
 Dark Heresy (Tabletop Game) / int_5ecdd585
type
Renegade Splinter Faction
 Delta Green (Tabletop Game) / int_5ecdd585
type
Renegade Splinter Faction
 Eclipse Phase (Tabletop Game) / int_5ecdd585
type
Renegade Splinter Faction
 Feng Shui (Tabletop Game) / int_5ecdd585
type
Renegade Splinter Faction
 Hunter: The Vigil – Dark and Light (Tabletop Game) / int_5ecdd585
type
Renegade Splinter Faction
 Star Realms (Tabletop Game) / int_5ecdd585
type
Renegade Splinter Faction
 Starfinder (Tabletop Game) / int_5ecdd585
type
Renegade Splinter Faction
 Waterdeep: Dragon Heist (Tabletop Game) / int_5ecdd585
type
Renegade Splinter Faction
 WitchCraft (Tabletop Game) / int_5ecdd585
type
Renegade Splinter Faction
 Armored Core: Nexus (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Beyond Earth (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Beyond Skyrim (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Chained Echoes (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Command & Conquer 3: Tiberium Wars (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Command & Conquer 4: Tiberian Twilight (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Command & Conquer 3: Tiberium Wars (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Command & Conquer: Tiberian Sun (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Deus Ex (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Dying Light 2 Stay Human (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Empire Earth (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Fallout 3 (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Fallout 76 (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Fire Emblem: The Sacred Stones (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 For the Enclave (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Guild Wars 2 (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Hitman 3 (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Jagged Alliance (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Killzone (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Lonely Wolf Treat (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Mafia III (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Marathon (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Mass Effect (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Midnight Fight Express (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Mount & Blade II: Bannerlord (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Old World Blues (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Perfect Dark (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 R-Type (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Resident Evil 2 (Remake) (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Resident Evil Village (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Skullgirls (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Spellstone (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Splinter Cell (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Star Control (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Star Trek: Bridge Commander (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Star Trek: Hidden Evil (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 State of Decay 2 (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 The Bureau: XCOM Declassified (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 The Frontier (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Thief (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Third Odyssey (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Time Crisis (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Vampyr (2018) (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 XCOM: Enemy Unknown (Video Game) / int_5ecdd585
type
Renegade Splinter Faction
 Aventures (Web Video) / int_5ecdd585
type
Renegade Splinter Faction
 Dark Harvest (Web Video) / int_5ecdd585
type
Renegade Splinter Faction
 Adapting to Night (Webcomic) / int_5ecdd585
type
Renegade Splinter Faction
 Serina (Website) / int_5ecdd585
type
Renegade Splinter Faction
 Beast Wars / int_5ecdd585
type
Renegade Splinter Faction
 Kenny Omega (Wrestling) / int_5ecdd585
type
Renegade Splinter Faction
 The Elite (Wrestling) / int_5ecdd585
type
Renegade Splinter Faction
 The Young Bucks (Wrestling) / int_5ecdd585
type
Renegade Splinter Faction