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Wrong Side All Along

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Normally, the villain or rival is trying to stop the hero For the Evulz or perhaps just out of selfishness. However, sometimes things are not what they seem. The mentor the party has come to trust throughout the story has been using them, or perhaps corrupting them, and the apparent Big Bad was actually trying to save the world and make the heroes understand them, or something of that nature. Expect a Heroic BSoD or three.
Normally, this can go several ways. The character can either undergo a Face–Heel Turn or Heel–Face Turn, they can become completely depressed and take their life, or they can refuse to believe the realization and continue helping their mentor as before. Alternatively, this may end up being subverted, and the villain is just trying to trick them by painting their favorite hero as a villain.
Subtrope of Evil Running Good; this is specific in that the antagonist is (also) a good guy (while that trope can have actual bad guys as antagonists). Compare Unwitting Pawn and Heel Realization.
Because of the nature of this trope, there will be spoilers.
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Nero ends up learning this the hard way in Devil May Cry 4 when the Order of the Sword are revealed to be Evil All Along. In fact, him meeting Agnus actually tips him off that they're not what they seem...
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Fire Emblem
Fire Emblem: Mystery of the Emblem starts with Marth travelling to put down a rebellion in Grust, who fought against him in the last war, on the behest of General Lang of Archanea. He quickly realizes that Lang has been horrifically abusing his position as head of the Grustian occupation (including kidnapping young girls for heavily-implied sex slavery) and sides with the rebellion against him. And then finds out that Hardin, his former ally and now king of Archanea, has become a Brainwashed and Crazy tyrant.
Played with in Fire Emblem: Genealogy of the Holy War, which shows the consequences of someone not realizing they're in this kind of story until it's too late. The Hero Sigurd's incursions into neighboring countries to help his friends unwittingly helps his own nation's corrupt nobles annex their territories, and they later assassinate the prince and frame Sigurd and his father for it. He gets back home just in time to deal with them... which plays right into the hands of another plot, as Arvis needed those nobles out of the way so he could take over The Empire Sigurd accidentally helped build. Sigurd barely has a few minutes to realize he was on the wrong side before Arvis kills him, leaving his son to clean up the mess after a Time Skip.
Per an interview, ultimately averted in regard to the Crimson Flower route of Fire Emblem: Three Houses. Part I of the game sets up the Church of Seiros — the major religious institution of the continent of Fodlan and the primary ally of the Officers' Academy, which is the educational institution that Byleth is made to teach at for the year — as well-intentioned yet far-reaching and suspicious, and its Archbishop, Rhea, ultimately turns out to have less-than-savory intentions for Byleth, hoping for their consciousness to be hijacked by that of her mother (and Fódlan's matron goddess), Sothis. While the church is ultimately less than ideal, their status as an all-encompassing evil is something of a Red Herring, and most routes of the game involve Byleth either siding with them directly (Silver Snow, where you reject Princess Edelgard's plans to bring Fódlan together under the Adrestian Empire's rule) or as a major ally (Azure Moon, where you side with Prince Dimitri of Faerghus, or Verdant Wind, where you side with Duke Claude of the Leicester Alliance); Furthermore, these routes all have the church undergo serious reforms, with the faith being far less encompassing than it was in the past. Siding with Edelgard paints her as a revolutionary and involves having her assimilate the other two countries under her rule and destroying the church entirely, proclaiming both it as well as the Children of the Goddess — the draconic race that Sothis, Rhea, Seteth, Flayn, and a few others are a part of — as being responsible for all of Fódlan's ills since time immemorial. While the game does not condemn Byleth for siding with Edelgard, even with the contradictions that her version of history has with the other routes or the misgivings that her allies have, the creators of the game noted in an interview that the game's worldbuilding is based on Silver Snow by default; In addition to being one of two routes that reveals Rhea's history and Byleth's origins, it is also the default path that the player is put on when they teach Edelgard's class — one has to go through several hoops to actually support Edelgard.
Played with again in Fire Emblem Engage, where a character went through this in the past. Specifically, The Hero Alear. They were the biological child of Sombron and, despite suffering horrible abuse, assisted his army as they had nowhere else to go and feared being killed as a "defect". (a fate that befell most of their siblings) Only a chance meeting with Lumera showed them there was another way, leading to them turning on Sombron but suffering a wound that forced them to hibernate for 1000 years.
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In the first episode of Alias, Sidney Bristow is happily working for the CIA and her boss/mentor Arvin Sloane. Then she finds out that she's not working for the CIA, she's working for a terrorist group against the CIA, and Sloane is in on it.
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On Star Trek: Enterprise, the Xindi plan to destroy Earth because godlike aliens told them that humanity would destroy them in the future. The truth is that the aliens want Earth destroyed so that The Federation will never form, as this Federation will stop the aliens from conquering the galaxy. Once Archer learns of this, he sets about convincing the Xindi of the truth, in order to save both races and the entire galaxy.
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Memory, Sorrow, and Thorn: The heroes are striving desperately to save the mortal races from the undying wrath of the Storm King, and are using the fragments of a book of prophecy to help them. The book was part of a very long con by the Storm King, strong in ill-will but weak in physical presence. By following the book's instructions they're filling out the recipe to bring him back from the dead and undo hundreds of years of history.
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In Ratchet & Clank: Going Commando, the titular duo are hired by MegaCorp to track down a mysterious thief and recover a stolen experiment. After defeating the thief in a Climax Boss fight halfway through the game, they learn that the thief is a former MegaCorp geneticist who stole the experiment, the Protopet, before it could be unleashed on the galaxy with devastating consequences. The game even manages to keep the same enemy mooks after switching antagonists, as Thugs 4 Less are quickly enticed with a better offer to change employers. It later turns out that not even MegaCorp are the real antagonists: the whole thing was an Engineered Heroics plot by Captain Qwark, and the heroes now have to save the galaxy from his stupidity.
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In Guild Wars Prophecies, when the heroes arrive in Kryta, they find the ruling White Mantle fighting rebels, the Shining Blade. They initally join with the Mantle, but when the Shining Blade point them to the truth about the Mantle — they're rounding up people identified as a threat to their "gods" to ritualistically execute them — they switch sides.
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In Sky High (2005), the cute older girl is playing him for a fool. She's actually a supervillain who got age reduced, and the imposing bully guy is actually just hot-headed.
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Altair spends most of Assassin's Creed killing key Templar figures on both sides of the Crusades. In the end, he is told that his master is a former Templar himself who was merely trying to eliminate the competition. While this doesn't turn him against the Assassins, he ends up fighting and killing his mentor.
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In Utopia, Wilson Wilson, the Conspiracy Theorist who becomes embroiled in a fight against a real conspiracy undergoes a Face–Heel Turn once he comes to the conclusion that the conspirators are right.
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In Golden Sun, Isaac goes on a quest to stop Saturos, Menardi, and Alex from unleashing Alchemy after being told that it's a dangerous force if misused. He learns late in the sequel that his mission to keep Alchemy sealed will actually cause the world to slowly decay into nothing, and that Saturos and Menardi were trying to save their hometown, Prox. Only by unleashing Alchemy can the world be saved. After he learns this, he immediately switches sides and helps Felix light the last beacon.
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Starwalker and her crew find out that the person who hired the Space Pirates was the avatar of our sun, who didn't like being used as a doorway 40 years ago (see Stable Time Loop), especially as using the star step drive shortens the life of stars. The crew realise that the star step technology is something that man is not supposed to know (especially as some people would probably look to optimize its destructive potential). They decide to rebel against the project, do what they can to heal the stars, and destroy all the copies of information that exist about the project.
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In Castlevania: Order of Ecclesia, Shanoa is instructed by her master Barlowe to cast the Dominus glyphs to permanently destroy Dracula. His other disciple Albus interrupts the ceremony and steals the glyphs, leaving her without memory. The game goes into a long trek to track him down and get the glyphs back. It turns out the glyphs were intended to revive Dracula, which was Barlowe's goal all along, and that casting it would kill her, which Albus was trying to prevent.
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In the anime version of Blue Dragon, the henchman of the Big Bad (after the Big Bad has supposedly been defeated) reveals that the party is being used to open up the Dark World by their leader. Of course, they don't realize this until after helping almost destroy the world.
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Fire Emblem: Mystery of the Emblem starts with Marth travelling to put down a rebellion in Grust, who fought against him in the last war, on the behest of General Lang of Archanea. He quickly realizes that Lang has been horrifically abusing his position as head of the Grustian occupation (including kidnapping young girls for heavily-implied sex slavery) and sides with the rebellion against him. And then finds out that Hardin, his former ally and now king of Archanea, has become a Brainwashed and Crazy tyrant.
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In Captain Marvel (2019), it turns out Carol Danvers and Nick Fury are unwittingly helping the genocidal and imperialistic Kree exterminate the Skrulls who, while themselves ruthless, were only trying to survive and find a new home for themselves. Carol in particular is pissed that she was being played like a cheap kazoo for the past six years, and pulls a Heel–Face Turn to stop them.
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This happened to Schlock's mother in Schlock Mercenary. Schlock's human grandmother was a slave trader and duped her amorph daughter into fighting the hero (Schlock's father), who was trying to stop her. Due to the unique nature of amorph biology, the fight ended up with the personalities of both Schlock's parents being destroyed and their bodies merging to produce Schlock.
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In the Spawn comics, Cogliostro only helped and mentored Spawn so that he could re-enter hell to become its ruler. For his real identity is Cain, the first killer and therefore the first hellspawn.
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His Mark On History: First Strong Messenger believes that he's been chosen by destiny to free the Strong Speakers and his homeland from being oppressed by the Griffon Empire. However, he's actually being manipulated by Nyarlathotep into triggering a massive war, which they intend to use to neutralize the entire continent of Taura as a threat to their overarching plans.
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Phantom Thief Jeanne, Finn Fish is the right-hand woman of Lucifer who has been using Jeanne, and the rival angel is trying to stop Finn as he knows that she has been possessed by evil.
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In the Phineas and Ferb Star Wars special, Candice, Baljeet, and Buford are Stormtroopers. The boys' motives aren't elaborated, but Candice gets a song about how she signed up in the name of law and order. After Phineas saves her life, she begins questioning things and asks Baljeet and Buford, if the Rebellion is so nice, does that mean the Empire might be the bad guys?
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In Bravely Default, Eternia and its Jobmasters, under the leadership of the supposed Big Bad Braev Lee, have been trying to usher in an era where people are not dependent on the elemental Crystals. The party opposes them, told by Exposition Fairy Airy that by awakening the Crystals, they would summon the Holy Pillar to cleanse evil from the world. As it turns out, Airy is in fact the true Big Bad and by awakening the Crystals, the party is further destabilizing all the different Luxendarcs while allowing Airy's father, Ouroboros, to devour their world. Either they over-awaken a Crystal to destroy it and set back the villain's plans by several centuries, or they resolve to persist, hoping that in the end they could face off against and destroy Ouroboros.
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Far Cry: Your sexy partner is liable to betray you. In the last episode, Jack considers Chronic Backstabbing Disorder a "human" trait that he has evolved from. Fortunately for him, his partner doesn't backstab him and instead the Mission Control you have for the entire game is the one who turns on you at the end of the game, although at a rather ill-conceived time.
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Far Cry 2: Jackal decides that after twenty years of selling low-grade firearms to unstable countries, he's had enough. You, an assassin hired to kill him, end up turning on your former contacts to help him isolate the warring factions (which have now banded together in order to take over Bowa-Sekao as warlords) from 2,000,000 human targets.
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Far Cry 3: The pirates and privateers who control the North and South Rook Islands deal in international human trafficking (slavery) and drugs. You dismantle their operations and kill the bosses so that the native tribe can retake their island. Then the tribe's leader tries to force you into killing your friends. If you do as she says, she'll murder you while you're having sex with her so that she can have undisputed worship from both islands, believing she did a favor by killing you in your prime rather than let you wither away from old age, and believing to have your child in her.
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Far Cry 4: Pagan Min, the "King of Kyrat", is a looney Fidel Castro with an iron grip on Kyrat. You join the local rebels to depose him from power, while also eliminating one of the dissenting rebel leaders to keep infighting at a minimum. While you're taking a vacation across the newly freed Kyrat, you discover that the surviving rebel leader has continued the dictatorship and shifted its priorities to an extreme. Sabal will order religious purges to restore Kyrat's strange and unique religion (and with Pagan's cult of personality permeating the country for decades, along with western influences thanks to the efforts of media rebels such as Rabi Ray Rana Rebel Air, that's pretty much 90% of Kyrat). Amita will attempt to turn Kyrat into one giant drug farm and conscripts children into her armies to enforce her rule.
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Far Cry 5: Somewhat disputable, but while it's clear that Joseph Seed's cult isn't doing a good job of "keeping people safe from the apocalypse", what with the various lieutenants screwing up on the keeping people alive thing, the citizens aren't paying attention to the local broadcasts on the global crisis which explains their panic — for example, Moscow getting nuked. Also, the Seeds are adamant that the player character is not what they seem, has a greater influence on the world than they realize, and is promptly screwing everyone over by destroying everything the cult tries to build.
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Far Cry: Each of the games features a deconstruction of being the "Good Guy" in a Crapsack World; there is no Big Good, there is only you.
Far Cry: Your sexy partner is liable to betray you. In the last episode, Jack considers Chronic Backstabbing Disorder a "human" trait that he has evolved from. Fortunately for him, his partner doesn't backstab him and instead the Mission Control you have for the entire game is the one who turns on you at the end of the game, although at a rather ill-conceived time.
Far Cry 2: Jackal decides that after twenty years of selling low-grade firearms to unstable countries, he's had enough. You, an assassin hired to kill him, end up turning on your former contacts to help him isolate the warring factions (which have now banded together in order to take over Bowa-Sekao as warlords) from 2,000,000 human targets.
Far Cry 3: The pirates and privateers who control the North and South Rook Islands deal in international human trafficking (slavery) and drugs. You dismantle their operations and kill the bosses so that the native tribe can retake their island. Then the tribe's leader tries to force you into killing your friends. If you do as she says, she'll murder you while you're having sex with her so that she can have undisputed worship from both islands, believing she did a favor by killing you in your prime rather than let you wither away from old age, and believing to have your child in her.
Far Cry 4: Pagan Min, the "King of Kyrat", is a looney Fidel Castro with an iron grip on Kyrat. You join the local rebels to depose him from power, while also eliminating one of the dissenting rebel leaders to keep infighting at a minimum. While you're taking a vacation across the newly freed Kyrat, you discover that the surviving rebel leader has continued the dictatorship and shifted its priorities to an extreme. Sabal will order religious purges to restore Kyrat's strange and unique religion (and with Pagan's cult of personality permeating the country for decades, along with western influences thanks to the efforts of media rebels such as Rabi Ray Rana Rebel Air, that's pretty much 90% of Kyrat). Amita will attempt to turn Kyrat into one giant drug farm and conscripts children into her armies to enforce her rule.
Far Cry 5: Somewhat disputable, but while it's clear that Joseph Seed's cult isn't doing a good job of "keeping people safe from the apocalypse", what with the various lieutenants screwing up on the keeping people alive thing, the citizens aren't paying attention to the local broadcasts on the global crisis which explains their panic — for example, Moscow getting nuked. Also, the Seeds are adamant that the player character is not what they seem, has a greater influence on the world than they realize, and is promptly screwing everyone over by destroying everything the cult tries to build.
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 Far Cry (Franchise)
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In Darker than Black, The Syndicate has been plotting for years to annihilate all Contractors, which Evening Primrose’s leader Amber, thought to be the Big Bad, was actually trying to stop. Not that surprising for the morally ambiguous Syndicate the protagonists work for, but it is surprising that The Syndicate also controls intelligence organizations (like MI6) and the police that the supporting characters work for, with Director Yoshimitsu Horai being a high-ranking member of the Syndicate and the other Big Bads, essentially making the majority of the cast bad guys.
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 Darker Than Black
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Played with again in Fire Emblem Engage, where a character went through this in the past. Specifically, The Hero Alear. They were the biological child of Sombron and, despite suffering horrible abuse, assisted his army as they had nowhere else to go and feared being killed as a "defect". (a fate that befell most of their siblings) Only a chance meeting with Lumera showed them there was another way, leading to them turning on Sombron but suffering a wound that forced them to hibernate for 1000 years.
 Wrong Side All Along / int_90f94684
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 Fire Emblem Engage (Video Game)
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In Wanted, the protagonist is brought into the Fraternity, a killer organization (with The Mentor, The Lancer, etc.), to kill the man who killed his father. It's eventually revealed that the bad guy is really his father and he was trying to stop the organization, which is shown to be corrupted. Cue Heel Realization and Storming the Castle.
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 Wanted
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The Hero Laughs While Walking the Path of Vengeance a Second Time is about a Fallen Hero and his party of the Betrayed using his time-travel fueled second chance to take revenge on a Crapsaccharine World which conned him into thinking he was in a stereotypical fantasy game, only to reveal at the very end that his side was composed of genocidal psychopaths who pinned the blame for their mass-murders of innocents on him.
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 The Hero Laughs While Walking the Path of Vengeance a Second Time
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Daimos: Richter spent most of the series despising humans and riding up the death toll to the millions for killing his father and dooming his people as refugees. Though he later finds out that it was a fellow Baam who killed him, his hatred for humans is not shaken, and he states he won't be satisfied until he cleanses the Earth and replaces them. Kazuya proves that his views are wrong by putting his body through relentless abuse and torture just to get a small chance at saving the refugees in Baam cryostatis. It is then that Richter's entire worldview changes - a mere human like Kazuya, doing his best to help him while being covered in scars (while the Baam King Olban abandoned them) makes him realize why his sister fell in love with the humans.
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Played with in Fire Emblem: Genealogy of the Holy War, which shows the consequences of someone not realizing they're in this kind of story until it's too late. The Hero Sigurd's incursions into neighboring countries to help his friends unwittingly helps his own nation's corrupt nobles annex their territories, and they later assassinate the prince and frame Sigurd and his father for it. He gets back home just in time to deal with them... which plays right into the hands of another plot, as Arvis needed those nobles out of the way so he could take over The Empire Sigurd accidentally helped build. Sigurd barely has a few minutes to realize he was on the wrong side before Arvis kills him, leaving his son to clean up the mess after a Time Skip.
 Wrong Side All Along / int_a68c19b8
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 Fire Emblem: Genealogy of the Holy War (Video Game)
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Mushoku Tensei: Jobless Reincarnation: Early on in his reincarnation, Rudeus begins receiving visions from an enigmatic being calling himself Hitogami who provides cryptic advice to him. Later on, he crosses paths with Hitogami's Arch-Enemy Orsted who ends up punching a hole in Rudeus's chest upon learning that he knows of Hitogami. Naturally, this leads Rudeus to be incredibly fearful of Orsted and thus more trusting of Hitogami. However, Rudeus eventually encounters a future version of himself who reveals to him that Hitogami is Evil All Along, and that in the Bad Future he came from he lost everyone he cared for thanks to him falling for Hitogami's manipulations.
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In the third Rebuild of Evangelion movie, poor Shinji falls victim to two instances of this: Just after having left the Renegade Splinter Faction of the organization he used to work for, he finds out that said organization, including his own father Gendo, has been plotting doomsday for quite a while, and, in fact, successfully set him up to cause it for them in a futile attempt to save his Love Interest, and, in fact, brought the two of them together for that exact purpose. Then, he gets told that he can fix the now nigh-inhabitable planet by obtaining a certain Artifact of Doom, which he sets out to get, having to fight his former roommate and friend Asuka in the process. When he actually gets his hands on the artifacts, they do, obviously, cause yet another near-apocalypse as Shinji stares in horror.
 Wrong Side All Along / int_aaa65d7e
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In the first volume of The League of Extraordinary Gentlemen, the League works for "M", speculated to be Mycroft Holmes. However, as it turns out, "M" is actually Moriarty, who is using them to expand his own criminal empire. The villain they're fighting against is still a monster, however.
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 The League of Extraordinary Gentlemen (Comic Book)
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In Jade Empire, you find out that your mentor has been playing you all along and basically used you as a tool to take over the empire... not that the Emperor was much better.
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 Jade Empire (Video Game)
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In The Magnus Archives, the Magnus Institute seems at first glance to be the "good guys" - for centuries, they've been accumulating knowledge of the occult in order to stop eldritch gods and their followers from ending the world. But then it turns out that they serve their OWN eldritch god, and are only foiling the other gods' apocalypse rituals in order to pave the way for an apocalypse ritual of their own. Which they successfully pull off in the season 4 finale, using Jon as the lynchpin.
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 The Magnus Archives (Podcast)
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Street Kings: Detective Ludlow and his team are supported by Captain Wander in their Cowboy Cop tendencies. A former partner of Ludlow then starts snitching to the antagonistic Captain Biggs from Internal Affairs before being killed in an apparently random shooting. Ludlow eventually discovers that Biggs's investigation was entirely justified and Wander has been running a wholesale extortion and murder racket behind Ludlow's back.
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1.0
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1.0
 Street Kings
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Stretch Armstrong and the Flex Fighters, where the titular trio learned that their sponsor Jonathan Rook is really the Stretch Monster, and so they've been helping a criminal mastermind throughout the first season. By the time they found this out in its season finale, they ended up becoming fugitives when Rook framed them for the attack on his tower, Rook Unlimited which was started by Rook himself when he tried to dispose of them after they come to realize his plans.
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1.0
 Stretch Armstrong and the Flex Fighters
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In Underworld (2003), Selene is a vampire soldier who has spent several centuries fighting the Lycans in order to avenge her family, and is unfailingly loyal to her maker and Parental Substitute, the Vampire Elder Viktor. But at the end of the film, she finds out that it was really Viktor who slaughtered her family, and couldn't bring himself to kill her because she reminded him so much of Sonja, his own daughter whom he had put to death for having a Lycan lover and becoming pregnant with his child; her death also instigated the war against the Lycans, who had been the vampires' slaves. He then blamed the Lycans for Selene's family's death, and had her trained to become a Death Dealer so that she could kill the Lycans, who just wanted justice for their inhumane treatment.
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 Underworld (2003)
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Kamen Rider Outsiders: The heroic Riders sided with a Knight Templar AI called Zein, believing it to be a Greater-Scope Paragon Benevolent A.I.. However, Zein is anything but benevolent to begin with as it plans to wipe out all human life to Take Over the World. The good guys find that out too late that they are enabling a tyrannical artificial intelligence planning to use an already Deadly Game and turn it into a humanity self-destruction game; by using unsuspecting players as cannon fodder to the villains. Zein's remaining followers can only react in utter despair, as the first season ends with the entire human race now under the mercy of a technological oppressor without any hope of opposing its tyranny.
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1.0
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 Kamen Rider Outsiders
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In Pokémon Mystery Dungeon: Explorers, the protagonists join the explorer from the future Dusknoir to stop Grovyle from stealing the Time Gears, with will freeze the planet in time, which Dusknoir went back in time to prevent. Turns out that Grovyle is the one trying to Set Right What Once Went Wrong, because even though there's temporary paralysis of the area where the Time Gear was taken, they need to be placed in Temporal Tower to stop Dialga from going Primal and avoid the Bad Future, and Dusknoir is working for Primal Dialga all along.
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1.0
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1.0
 Pokémon Mystery Dungeon: Explorers (Video Game)
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She-Ra and the Princesses of Power:
The opening plot has young protagonist, Adora, finding out she was raised and trained to fight and serve the oppressive, conquering Horde Empire, and her mentor Shadow Weaver was using and grooming her all along. After she discovers she is the next chosen one to become She-Ra, she joins the rebellion against them.
This done again in Season 4. Adora finds out that the role of She-Ra isn't a heroic one. The chosen one is meant to be a key to a super weapon used to destroy other planets. The First Ones, whom created She-Ra weren't good, wise and holy people, but intergalactic conquerors, no different than the Horde Empire, if not worse.
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 She-Ra and the Princesses of Power
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At first it's not clear that Atlantis: The Lost Empire even has an antagonist. Then Milo finds out that the rest of the crew led by Rourke are actually mercenaries out to steal Atlantis' Power Crystal so they can sell it to the highest bidder, and are (at first) willing to doom the Atlanteans in the process. Fortunately, all of them but Rourke and Helga (and their small army of mooks) make a Heel–Face Turn.
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 Atlantis: The Lost Empire
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In Dan The Man, Dan spends the first few stages fighting a La Résistance group made of red ninjas, and eventually defends the kingdom from a dragon. Turns out the dragon was trying to rescue its child, which was being used to power the kingdom, and the resistance is trying to fight the tyranny and greed of the kingdom's rulers. It then pulls this again when the resistance turns out to be as brutal as their enemies.
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In Spec Ops: The Line, Captain Walker and his team are frequently the sole reason things get worse in Dubai. They destroy the water supply, massacre civilians, and commit other atrocities in the name of fighting evil. Whoops.
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 Spec Ops: The Line (Video Game)
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Indiana Jones and the Last Crusade. Indiana Jones fights against the Brotherhood of the Cruciform Sword during the film. It turns out they're just trying to protect the Grail's hiding place from the Nazis. The person who sent Jones on the mission to find the Grail, Walter Donovan, is really the Big Bad and a Nazi sympathizer (well, kind of).
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 Indiana Jones and the Last Crusade
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This is the twist in The Sword of Good. The "good guys" are actually agents of The Empire keeping a malignant status quo, while the "villain" is one of the only people in the setting who sees that it's broken and is trying to do something about it. Tellingly, the hero is only able to unleash the Sword's full power when he cuts down his former allies.
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Voltes V: Prince Heinel spent his entire life believing that his father was a traitor and he committed a crime against Boazania. He became a fervent nationalist as a result and swore to do whatever it took to bring back honour to his name. When Heinel fails to take over Earth, his cruel uncle, the Emperor, humiliates and exiles him. Undeterred, Heinel returns to Boazania, and he finds out that his father is alive. Both son and father are shocked to see that the former has horns while the latter doesn't - this means Heinel is the son of a Hornless Boazanian, who are the Slave Race - and he understands that his father's "crime" was actually trying to liberate the slaves of the planet. He has a breakdown on the spot and decries ever taking part in the war in the first place.
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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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Index All Along
 Kite (1998) / int_b9bb56bb
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 Origin: Spirits of the Past / int_b9bb56bb
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 His Mark On History (Fanfic) / int_b9bb56bb
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 Captain Marvel (2019) / int_b9bb56bb
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 Night of the Comet / int_b9bb56bb
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 Mobile Suit Gundam: Hathaway's Flash / int_b9bb56bb
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 Sienkiewicz Trilogy / int_b9bb56bb
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 The Sword of Good / int_b9bb56bb
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 Utopia / int_b9bb56bb
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 Vampire: The Masquerade (Tabletop Game) / int_b9bb56bb
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 Goonya Monster (Video Game) / int_b9bb56bb
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 Jagged Alliance (Video Game) / int_b9bb56bb
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 Lair (Video Game) / int_b9bb56bb
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 Pokémon Mystery Dungeon: Explorers (Video Game) / int_b9bb56bb
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 South Park: The Fractured but Whole (Video Game) / int_b9bb56bb
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 Wanderers of Sorceria (Video Game) / int_b9bb56bb
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 Dan The Man (Web Animation) / int_b9bb56bb
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 DuckTales (2017) / int_b9bb56bb
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 The LEGO Movie 2: The Second Part / int_b9bb56bb
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