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Rogue Protagonist

 Rogue Protagonist
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Alright, The Hero has saved the world, paid off his debts, and made time with that girl in the blue dress. His story is done, the credits have rolled, and there was no "To Be Continued", but what's this about a Sequel? What could the guy be in for now?
...Wait, who are these new people? And where's the character from the original?
WHAT?! He's a villain now?! What happened? He went rogue.
Usually, the new main character is Locked Out of the Loop and doesn't know something that the original character does, or the other way around (or perhaps both), and they're at odds over it. Of course, there might be other reasons, but in these cases, it usually ends with the new characters and the original cast working along the same side.
Alternatively, the original character really has gone to the dark side for whatever reason. (Or may have been there the whole time...)
This often appears in Video Games, as a previous main character may be an excellent Final-Exam Boss (thus overlapping with Dueling Player Characters) or give the player A Taste of Power from their side as an Antagonist.
While it can appear that way, this isn't in effect in a P.O.V. Sequel, given that said P.O.V. Sequel is a retelling of the original story.
A Sub-Trope of Sudden Sequel Heel Syndrome; also compare with Not as You Know Them. Also note how these heroes seem to avert the Bag of Spilling. See also Previous Player-Character Cameo, when the old PC isn't a major antagonist.
Compare and contrast with Fallen Hero and Role-Reversal Boss. Not to be confused with a hero who happens to be a Rogue. Or Rogue herself. Has nothing to do with Rogue One either. Enemy Without does
NOT count, unless used as a subversion (via deliberate trick on the viewer).
WARNING: Expect spoilers.
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Before Divinity II (Canonically) in Divinity: Original Sin II, Lucian turns out to be The Man Behind the Man of Magister Dallis, who is working towards the same goals as her. Sure enough, Lucian is one of the final bosses of Original Sin II, though not the TRUE Final Boss (that honour goes to Braccus Rex, who is the only one who must be defeated.)
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Clyde from Vigilante 8 turns heel in the sequel. His ending in the first game has him finding the villain's bracelets in a men's bathroom, and it possesses him when he puts them on.
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In general, this plot tends to happen a lot in tokusatsu crossovers, with one set of heroes believing the other to be villains until they eventually discover the truth. Some examples include Gekisou Sentai Carranger vs. Ohranger (in which the monster tricks the Carrangers into taking his side against the Ohrangers), Gokaiger Goseiger Super Sentai 199 Hero Great Battle (in which the Goseigers and Gokaigers come into conflict over possession of the Goseiger Ranger Keys), Tokumei Sentai Go-Busters vs. Kaizoku Sentai Gokaiger: The Movie ( in which the Gokaigers work for Zangyack while trying to undermine them from inside), and Kamen Rider X Super Sentai Superhero Taisen (in which Tsukasa and Marvelous only pretended to kill the other heroes to lure out the villains).
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In Tactics Ogre, there is a Gaiden Game for the Game Boy Advance called The Knight of Lodis. Whatever happened to the titular Knight of Lodis? He becomes a Climax Boss in Tactics Ogre: Let us Cling Together, essentially an antagonist, but not the antagonist.
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In Devil May Cry 4, Dante is an example, showing up as a villain right out of hell, and making himself a serious enemy to Nero, the new protagonist. They do end up fighting for a similar cause later, especially when it's revealed that the guy that Dante gunned down, and who got better, is the Big Bad.
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Might and Magic VII: A late-game reveal is that the eight mysterious Visitors that the intro showed breaking up into two quarrelling groups are the protagonists of III, their spaceship turning out to not have crashed before IV as Corak thought and instead going from world to world. One group end up as the leading villains of the game. Either group can end up as the leading antagonists of the game, depending on if the protagonists of VII align with Bracada or Deyja.
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Chronologically inverted since Tales of Berseria is a prequel to Tales of Zestiria. Eizen succumbs to malevolence between games, turns into a dragon, and has to be put down by Sorey and his party, while Laphicet becomes the dragon Maotelus, gets corrupted, and has to be purified by the same.
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In a fashion in Dark Souls III, in relation to the Final Boss. The Soul of Cinder is stated to be the corporeal manifestation of everyone that ever Linked the Fire, which could potentially include the Chosen Undead from Dark Souls and the Bearer Of The Curse from Dark Souls II.
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In Final Fantasy IV: The After Years, the kingdom of Baron is once again aggressively invading its fellow nations in order to take the Crystals. However, this time, the king of Baron is Cecil... a Brainwashed and Crazy Cecil.
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Umineko: When They Cry: Subverted. While Bernkastel, who was originally a part of Rika, the protagonist of Higurashi: When They Cry, became this after going through a "Groundhog Day" Loop and becoming an amalgamation of all the pain from it, Word of God states that Bernkastel is essentially an Enemy Without, being purged from Rika’s consciousness after the Dice Killing Chapter.
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Subverted in Metal Gear Solid 2: Sons of Liberty. At the start of the Plant chapter, Raiden is repeatedly told that the leader of the terrorists is Solid Snake. Ten minutes of gameplay and one Paper-Thin Disguise later, you realize you were an idiot for thinking it was possible.
In theory, this is supposed to be a lot less obvious. In the US version, Solid Snake and the actual terrorist leader, Solidus Snake, have different voices. In the Japanese version, they have the same actor, leading to more confusion - you listen in on the terrorist leader's plans, only to hear Solid Snake's voice. Snake is also explicitly lying to the main character from their first meeting. In Japan, it's a legitimate possibility for the first half of the game.
If we look at the series' timeline, Naked Snake/Big Boss is one. He's the hero in Metal Gear Solid 3: Snake Eater, Metal Gear Solid: Portable Ops, Metal Gear Solid: Peace Walker, Metal Gear Solid V: Ground Zeroes and Metal Gear Solid V: The Phantom Pain, and the Big Bad of Metal Gear and Metal Gear 2: Solid Snake. And reappears in Metal Gear Solid 4: Guns of the Patriots's epilogue to tie up the loose ends.
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You learn of a possessed and evil character in Diablo II, called the Dark Wanderer. As it turns out, he's the player character of the first Diablo.note More specifically, the warrior class. The other two classes also turned rogue, including the rogue — the Rogue became the Wake-Up Call Boss Blood Raven, and the Sorcerer became the Act II boss The Summoner.
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Felix is an opponent to Isaac's group in the first game, and The Stinger for the first game makes it fairly clear that you'll be playing as Felix in TLA. Neither Isaac's goal nor Felix's has changed, so they're still at odds. Effectively, it's the player who's gone rogue.
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Sasuke in Part 2 of Naruto, who's left the village and joined Orochimaru, making several attempts on the lives of his former friends. He takes a few trips through the Heel–Face Revolving Door over the course of Part 2 before ending up as the True Final Boss of the story, his narrow defeat at Naruto's hands resulting in a Heel–Face Turn that actually sticks, as seen in the sequel series where he becomes The Mentor to Naruto's son.
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Lore for the Twitch Plays Pokémon runs have it so that the first player character, Twitch Plays Pokémon Red's Red, eventually goes insane from the Voices in his head and becomes the zealous emissary of the Helix fossil by the time of Twitch Plays Pokémon Crystal. When he is fought on Mount Silver the end of the run by the new anti-god protagonist AJDNWW, it's portrayed as a clash of ideals from one "Host" to another.
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The sympathetic and seemingly good-natured protagonist of MechWarrior 4 is revealed to have turned into a cruel despot in the expansion pack, and serves as a Disc-One Final Boss. In his case, it may have been Villainous Lineage, as he obtained the throne by overthrowing his evil dictator cousin.
Also, this is an explicit follow-up to one of two possible endings to the original game. Presumably, a sequel to the other ending would not feature him as a villain.
Word of God states that he was smear-campaigned by Katrina Steiner-Davion's loyalists and a vast majority of people bought it. Whether this means the events of Black Knight are actually what happens or some kind of Steiner propaganda is still up for debate (especially given the game's second half).
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Attack on Titan: Eren Jaeger in Season 4, going from killing the Titans to save humanity to controlling the Titans to wipe out humanity.
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Dark Forces Saga:
In Jedi Knight: Dark Forces II: Mysteries of the Sith, the player character for most of the game is Mara Jade Skywalker, and the previous player character Kyle Katarn falls to the Dark Side for the final boss fight.
Jedi Knight: Jedi Academy also has Katarn as the final boss for one of the endings. This time, however, he hasn't fallen to the Dark Side; you have.
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Also may have happened in Golden Sun: Dark Dawn, since Felix hasn't been seen since he left Vale shortly after the Golden Sun.
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24:
Jack becomes one for the last arc of Day 8, in which Chloe and the rest of the trustworthy staff at CTU have to keep him off the warpath in addition to stopping the main villains of the season. He snaps back to normal by the finale, but the sequel mini-series 24: Live Another Day shows that he's still seen by the public as this. Namely, even though he's trying to protect the President from being assassinated (again), due to his previous actions everyone's become convinced that he's the one behind the attack.
A couple seasons before that, it's Tony who goes into rogue solo revenge mode.
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Taylor, the hero of Planet of the Apes (1968), only appears in a few scenes of the sequel, Beneath the Planet of the Apes, and is a lot more unstable as the occasional ally, occasional enemy of the new protagonist, Brent.
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Elden Ring has an In-Universe variant. You aren't the first Tarnished to seek to become Elden Lord, but by the time the playable Tarnished shows up, most of their predecessors have, for one reason or another, abandoned their quest and are no longer guided by Grace, with the only holdouts being yourself, Sir Gideon Ofnir, Goldmask, and Hoarah Loux. And while some have just given up on the whole 'Elden Lord' deal and are still generally nice people (Nepheli Loux and Sorceror Rogier, for example), others have become villainous. The best example is Festering Fingerprint Vyke, who was once the prime candidate for Elden Lordship but has since fallen to the Frenzied Flame. Bernahl was another Tarnished close to becoming Elden Lord, but turned against the Erdtree to throw in with Volcano Manor, which has the explicit goal of murdering Tarnished so that no one will ever fix the Elden Ring. Sir Gideon Ofnir himself becomes one when something inside the Erdtree breaks his spirit and makes him believe that it's impossible to become Elden Lord.
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The "Warriors of Darkness" you encounter in the 3.1 story in Final Fantasy XIV? They used to be the Warriors of Light just like you (and Word of God confirmed that the player character stand-ins shown in the 2.0 trailers are their own characters) and have forsaken the light in favor of the dark.
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Luc Deveraux spends most of the Universal Soldier series as The Hero. He becomes the villain of Universal Soldier: Day of Reckoning, leading a renegade army of UniSols, Colonel Kurtz-style.
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Golden Sun:
Isaac in Golden Sun: The Lost Age is an unseen antagonist to the game's main character, Felix. Felix intentionally avoids contact with Isaac, because he knows they're working against one another, and wishes to avoid a fight — until Felix's supposed allies Karst and Agatio try to kill Isaac, at which point the groups are forced into an uneasy alliance (and eventually team up for real once Felix convinces Isaac he's right).
Felix is an opponent to Isaac's group in the first game, and The Stinger for the first game makes it fairly clear that you'll be playing as Felix in TLA. Neither Isaac's goal nor Felix's has changed, so they're still at odds. Effectively, it's the player who's gone rogue.
Though Felix does it in reverse, and Jenna and Sheba do it without the player realising it at the time: Felix was an antagonist who then became the protagonist, and Jenna and Sheba were both prisoners who needed to be rescued as far as Isaac knew in the first game, but in the second game it turns out that Jenna was helping of her own free will and Sheba joined Felix's quest because she wanted to get to Jupiter Lighthouse.
Also may have happened in Golden Sun: Dark Dawn, since Felix hasn't been seen since he left Vale shortly after the Golden Sun.
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Isaac in Golden Sun: The Lost Age is an unseen antagonist to the game's main character, Felix. Felix intentionally avoids contact with Isaac, because he knows they're working against one another, and wishes to avoid a fight — until Felix's supposed allies Karst and Agatio try to kill Isaac, at which point the groups are forced into an uneasy alliance (and eventually team up for real once Felix convinces Isaac he's right).
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Lloyd Irving in Tales of Symphonia: Dawn of the New World is seen as a murderer at first, in stark contrast to his ideals in the first game. Emil hates him for killing his parents in a brutal massacre of Palmacosta. Of course, he's not really a villain. The Lloyd who committed those crimes was Decus wearing a disguise.
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Task Force 141, one of the main forces of good in Call of Duty: Modern Warfare 2, becomes disavowed by the end of that game due to Soap killing General Shepherd, and spend about the entirety of Call of Duty: Modern Warfare 3 working unofficially until their eventual reinstatement by NATO.
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Hal Jordan during Kyle Rayner's first days as Green Lantern, who's been possessed by the Fear Entity, Parallax.
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First in Divinity II: The Dragon Knight Saga, Lucian is the Final Boss of the normal route.
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In The Elder Scrolls V: Skyrim, it's shown that following the events of Shivering Isles the Hero of Kvatch has become the Daedric Prince Sheogorath. While he's not a villain per se, as the god of madness and the physical embodiment of Chaotic Neutral he's not a good guy either, considering his predecessor performed a Colony Drop on Morrowind out of either boredom or a minor slight.
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During the events of Sly Cooper: Thieves in Time, it is revealed that Penelope has undergone a Face–Heel Turn and is working with the game's Big Bad Cyril Le Paradox.
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 Sly Cooper: Thieves in Time (Video Game)
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Rogue Protagonist
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Jill Valentine in Resident Evil 5 as a result of being Brainwashed and Crazy by Wesker.
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 Resident Evil 5 (Video Game)
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Rogue Protagonist
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Played straight in Disgaea 2: Cursed Memories, however, which features Laharl and Etna, the respective protagonist and deuteragonist of the first game, as plot-relevant antagonists. Etna wants to kill Overlord Zenon in order to take over his Netherworld, which directly opposes Adell's goal of defeating Zenon to restore the Netherworld back to a human world. Laharl, on the other hand, just wants Etna (who has joined Adell's party at this point) to come back to work for him again.
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 Disgaea 2: Cursed Memories (Video Game)
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Rogue Protagonist
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In .hack//G.U., Kite's avatar from the first games is used as an evil AI. Also, Elk shows up as Endrance, who plays the part of a villain for a good portion of the game.
 Rogue Protagonist / int_6418fc5
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1.0
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 .hack//G.U. (Video Game)
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Rogue Protagonist
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Terminator Genisys: The T-3000 is none other than John Connor.
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 Terminator Genisys
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Rogue Protagonist / int_679edf73
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Rogue Protagonist
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In Slender: The Arrival, the Chaser is revealed to be the Brainwashed and Crazy protagonist from the first game, Kate.
 Rogue Protagonist / int_69838404
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 Slender: The Arrival (Video Game)
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In Silent Scope EX, Falcon, the series' protagonist, and Jackal, one of the other protagonists of the second game, can be one of the suspects attempting to assassinate the President.
 Rogue Protagonist / int_69977d0c
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 Silent Scope (Video Game)
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Yakuza 0: Majima inverts this since he starts out as an antagonist in Yakuza and continues on from there as Kiryu's frenemy. Here, he starts out as much kinder and softer in comparison to the Mad Dog of Shimano he would become.
Kiwami 1 expands on this in that his Mad Dog persona is just an act he puts up to keep his head on his shoulders in the yakuza world. He also uses every style he had in 0 to further cement his status as Kiryu's nemesis and rival.
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 Yakuza 0 (Video Game)
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Kiwami 1 expands on this in that his Mad Dog persona is just an act he puts up to keep his head on his shoulders in the yakuza world. He also uses every style he had in 0 to further cement his status as Kiryu's nemesis and rival.
 Rogue Protagonist / int_6c6852c5
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 Yakuza (Video Game)
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Angela Deth was one of the four party members in Wasteland and a supporting character in Wasteland 2, but in Wasteland 3 she's an Anti-Hero whose Black-and-White Insanity causes her to antagonize the Player Character for trying to placate the morally gray Patriarch and her actions potentially instigate a Civil War among the Desert Rangers and Colorado as a whole unless you met the requirements for the Golden Ending.
 Rogue Protagonist / int_6f70ad52
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 Wasteland (Video Game)
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Rogue Protagonist
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Downplayed by Aurelia Hammerlock from the Borderlands series. In Borderlands: The Pre-Sequel!, she is an Affably Evil Villain Protagonist who even calls Jack out when he goes too far. Come Borderlands 3, and she's a much nastier NPC who ends up signing on with the Calypsos and being the Arc Villain of Eden-6.
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 Borderlands (Video Game)
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Rogue Protagonist
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Star Trek: Deep Space Nine: A minor example in Michael Eddington. Once the Starfleet officer sent to handle station security, he defects to the Maquis terrorist organization.
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 Star Trek: Deep Space Nine
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In [PROTOTYPE], Alex Mercer fought to stop the infected and Blackwatch from destroying New York. [PROTOTYPE 2] has him spreading the infection, including to the new player character, James Heller. The reasons for his Face–Heel Turn, given in a Motive Rant towards the end and a prequel comic, seem to be out of line with his characterization at the end of the first game. The best explanation is that he ended up seeing things that convinced him that Humans Are the Real Monsters.
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 [PROTOTYPE] / Videogame
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This is how you appear to your former squadmates in Mass Effect 2, seeing as how you're currently working for Cerberus, a terrorist group whose members were shoot-on-sight enemies in the first game. Ashley and Kaidan outright refuse to go with you because of it, and Tali rejoins with serious reservations about the Normandy's Cerberus-comprised crew (they attacked her people, so It's Personal). Subverted in that Shepard eventually leaves Cerberus (not to mention people like Admiral Hackett essentially considered Shepard a shadow asset the entire time), Garrus and Wrex trust Shepard without a second thought (although Garrus is reasonably concerned about the Cerberus connection), and everyone else eventually trusts Shepard once again. In fact, the only one who you can possibly kill over this is the Virmire survivor in Mass Effect 3, and even that is hard to do in standard gameplay.
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 Mass Effect 2 (Video Game)
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Rogue Protagonist
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In Streets of Rage 4, one of the bosses you fight in the second half is Max, one of the playable characters from the second game, seemingly being mind-controlled by the Big Bads.
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 Streets of Rage (Video Game)
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Rogue Protagonist
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In The Abundance, the sequel to Faith and Doubt, five of the Mane 6 become the Queens of Harmony, overthrowing the alicorn sisters, and imposing a totalitarian rule upon Equestria to achieve true harmony. As it turns out, they were manipulated by the five abstracts, who were in turn manipulated by the abstract Doubt, who wanted vengeance upon Faith for stealing her name.
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 Faith and Doubt / Fan Fic
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Rogue Protagonist
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Frank Miller's take on Batman is a cyclic and tragic example in hindsight. In Batman: Year One, he's definitely a hero... until the events of All-Star Batman & Robin, the Boy Wonder, in which he's a cop-killing, child-abusing sociopath who's only "good" because of the people he's up against. Then, by Batman: The Dark Knight Returns, he returns as a gruff but still heroic individual... only to lapse into the terrorist "hero" seen in The Dark Knight Strikes Again.
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 Batman (Comic Book)
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Rogue Protagonist
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Lenneth Valkyrie from Valkyrie Profile is essentially the main antagonist (from Wylfred's eyes) in Valkyrie Profile: Covenant of the Plume, and can be the final boss (depending on which ending is viewed.)
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 Valkyrie Profile (Video Game)
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Rogue Protagonist
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Pizza Tower: In a meta sense. This tweet by the developer discusses a supposed prequel to the game that places Pizza Tower's protagonist, Peppino, as the villain to a Mario-esque character named Pizza Boy, referencing how Wario started as a villain and eventually gained his own series. However, while Wario never again clashed with his heroic counterpart in his personal series, it is ultimately revealed that the mastermind behind Pizza Tower's plot is Pizzahead, who is heavily suggested (and externally confirmed) to be a grown-up version of Pizza Boy who became too protective of the tower and plotted to get even with Peppino.
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 Pizza Tower (Video Game)
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Sengoku Youko: The first part of the story ends with Jinka trying to unlock too many levels of power at once and having his energies go out of control, reducing him to a mindless "divine beast" that brings death to its surroundings. After a Time Skip, the story picks up with Senya, a Tyke-Bomb antagonist from the first arc as the new protagonist, who's looking for a way to save Jinka without suffering the same fate.
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 Sengoku Youko (Manga)
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Rogue Protagonist
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In the True Mastermind Edition of Time Crisis 5, Robert Baxter from Time Crisis II is revealed to be the Big Bad.
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 Time Crisis (Video Game)
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A heavily downplayed and sympathetic variation of this exists in the My Little Pony: Equestria Girls franchise: The first film and Rainbow Rocks both have Princess Twilight Sparkle as the protagonist/deuteragonist. Friendship Games features the character's native human self as a Nice Girl and Token Good Teammate of the Shadowbolts who is reluctantly Forced into Evil by being blackmailed into helping the real villain Principal Cinch...and suffers from the misfortune of turning into a she-demon called Midnight Sparkle, who serves as the final villain, because she was peer-pressured by Cinch and the Shadowbolts into releasing the magic from her amulet so that they can win the Friendship Games through underhanded means! Fortunately, in the end, she receives a Heel–Face Turn, courtesy of Sunset Shimmer saving her from her curse, and stays firmly on the side of good starting with The Legend Of Everfree!
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 My Little Pony: Equestria Girls
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Rogue Protagonist
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Chika's Bizarre Adventure: One of the early twists in the Love Live! Sunshine!!/JoJo's Bizarre Adventure crossover is that µ's, the protagonists of the previous series Love Live!, are not only Stand-users like Aqours but are now major antagonists, starting with Kotori using her armor stand Catch the Wind to pluck You Watanabe from the air in an effort to kill her. It's later revealed that µ's is fighting to protect their leader Honoka, hunting down whoever froze her alive and keeping anyone from removing the Origin Arrow injected in her body.
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 Chika's Bizarre Adventure (Fanfic)
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Rogue Protagonist
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Vanessa/Vanny was the protagonist of Five Nights At Freddys VR Help Wanted, wherein she becomes partially possessed by the Virtual Ghost of Serial Killer William Afton. She returns as the Big Bad of Five Nights at Freddy's: Security Breach, acting as Afton's Jack the Ripoff.
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 Five Nights at Freddy's VR: Help Wanted (Video Game)
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Rogue Protagonist
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Kain, the main character from Blood Omen: Legacy of Kain, is the Big Bad of the sequel Legacy of Kain: Soul Reaver. In a twist on the trope, Kain was already a Villain Protagonist in his own game, which was very much a story of Evil Versus Evil.
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 Blood Omen: Legacy of Kain (Video Game)
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Rogue Protagonist
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In Jedi Knight: Dark Forces II: Mysteries of the Sith, the player character for most of the game is Mara Jade Skywalker, and the previous player character Kyle Katarn falls to the Dark Side for the final boss fight.
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 Jedi Knight: Dark Forces II (Video Game)
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Xenoblade Chronicles 3: Melia and Nia (main party members from Xenoblade Chronicles 1 and Xenoblade Chronicles 2, respectively) appear as the queens of Keves and Agnus, with the two nations fighting a bloody Forever War for no clear reason, showing no concern over sending their subjects to die in droves. Subverted, as the queens are actually robot Puppet Kings used to control the two nations by the real villains, Moebius. The real Melia and Nia are still firmly on the side of good, ultimately playing key roles in freeing the world from Moebius.
In the DLC story, Future Redeemed, Alvis, the god-like AI who lead Shulk to save the world in Xenoblade Chronicles 1, returns (now calling himself Alpha). He intends to destroy the world of Aionios and everyone who originated from the Bionis or Alrest, planning to create a new world in its place that he considers "old life" unworthy of. Justified, as he is now following his programming with cold logic, with Pneuma, Logos, and Klaus no longer around to give him a moral framework. Ultimately Zigzagged, as a part of him eventually splits off to form A: Essentially, his conscience. A is composed of his memories of the time with Shulk, still on the side of good, and ultimately acknowledged by Shulk to be the true "Alvis".
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 Xenoblade Chronicles 3 (Video Game)
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Agent Washington in Red vs. Blue, who makes the switch between seasons 6 and 8. Though arguably he ends up not a villain but as an Anti-Hero Antagonist, as he has understandable non-evil (if selfish) goals which just end up opposing the other main characters' goals. Wash risks his life to obtain the evidence needed to implicate The Director and is captured while attacking a secure facility. Unfortunately, the person with the evidence would rather use it to rescue his friend than turn the evidence in to the authorities. So Wash is arrested. He then shifts to the mentality of "Being a hero sucks, I am just gonna clear my name and move on", which puts him in direct opposition with the Reds and the Blues. He does take a level in ruthlessness, as he shot Donut and Lopez just to prove a point, and threatens Simmons and Doc with torture. He has a Heel–Face Turn that sticks after the finale, when the Blood Gulch Crew saves him from the Meta, and helps him escape the UNSC by disguising him as Church.
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 Red vs. Blue (Web Animation)
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Yomi in Ga-Rei -Zero-. From helpful mentor and friend of Kagura in the prequel anime to the Big Bad in the beginning of the manga. And then an even bigger bad near the end of the manga. She does lament her situation.
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 Ga-Rei -Zero-
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Metroid Prime: Federation Force: Samus Aran is the final boss of the game after having been captured and brainwashed by the Space Pirates, transformed into a giant for good measure. Thankfully, she's stuck in the Morph Ball the entire time, so the fight isn't as hopeless as you'd think.
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 Metroid Prime: Federation Force (Video Game)
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Mario goes from rescuing his girlfriend in Donkey Kong to holding the big ape hostage and playing the bad guy to his son in Donkey Kong Junior.
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 Donkey Kong (Video Game)
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In Suicide Squad: Kill the Justice League, Batman went from being the Hero Protagonist of the Arkham series to a Brainwashed and Crazy minion of Brainiac.
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 Suicide Squad: Kill the Justice League (Video Game)
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Ethan Waber in Phantasy Star Universe: Ambition of the Illuminus. The events that cause him to go rogue are detailed in the online comic Shadow of the Arkguard.
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 Phantasy Star Universe (Video Game)
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The Tekken series has this a lot. Kazuya is the protagonist in the first game but becomes the antagonist from the second game onward. Jin, Kazuya's son, is the protagonist in the third game, and remains in the role for the next two games before finally taking an antagonistic turn in Tekken 6. The main distinction here is that Kazuya was always meant to be a villain from Day 1, whereas Jin turns out to be a Well-Intentioned Extremist trying to combat a greater evil brought to life by his family's ongoing bloody feud.
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 Tekken (Franchise)
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Mega Man Zero sets this up with Mega Man X apparently leading the slaughter of an untold number of reploids. It's subverted, but you knew that.
Also, Omega of Zero 3. Exactly how? He is the real Zero (well, his original body with another mind) and the player character of the Zero series was merely a reproduction (or rather, the mind of the original Zero in a duplicate body).
When the Zero series was in production, the real X was in fact supposed to be the Big Bad. However, Executive Meddling forced Keiji Inafune to continue the X series beyond X5, which also forced him to alter the Zero series a bit.
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 Mega Man Zero (Video Game)
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Whoever the player picks between Gray and Ashe in Mega Man ZX Advent has to fight the opposite-gendered character from the first game, that being Aile and Vent respectively. They both believe the other wants to claim a nearby Model W, and when the fight concludes, they realize they're on the same side and team up for the rest of the game.
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 Mega Man ZX (Video Game)
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In Ace Combat Zero: The Belkan War, the True Final Boss of the Brutal Bonus Level is Mobius 1, the protagonist and Player Character of Ace Combat 04: Shattered Skies (which should be chronologically impossible, as Ace Combat 04 takes place ~10 years after Ace Combat Zero, and Mobius 1 officially starts Ace Combat 04 as a newbie pilot). Later games with similar Boss Rush modes also add Scarface One of Ace Combat 2 and Blaze from Ace Combat 5: The Unsung War.
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 Ace Combat Zero: The Belkan War (Video Game)
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The Immortal Game's plot is kicked off when the villains use an Artifact of Doom to transform Twilight Sparkle into the Ax-Crazy Blood Knight Nihilus, who ends up serving as the story's first Climax Boss — the heroes have to defeat her before they even think about going after the other villains.
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After the Finale of The Legend of Heroes: Trails of Cold Steel II, there's a brief Divertissement chapter where you control the main character from The Legend of Heroes: Trails from Zero and Trails to Azure. The segments end with a boss fight against Rean, the protagonist of Cold Steel, having been forced into helping subjugate Crossbell due to his reputation as a war hero. He's not exactly happy about his new job, though.
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 The Legend of Heroes: Trails of Cold Steel (Video Game)
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Jedi Knight: Jedi Academy also has Katarn as the final boss for one of the endings. This time, however, he hasn't fallen to the Dark Side; you have.
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 Jedi Knight: Jedi Academy (Video Game)
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Rogue Protagonist
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In Jade Cocoon, Levant, the main character of the first game, is one of the second game's final bosses.
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 Jade Cocoon (Video Game)
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Fire Emblem Warriors: Three Hopes is a spin-off that does this by way of being an Alternate Timeline to the events of the mainline game Three Houses. Here, the protagonist is Shez, a mercenary who is implied to have died in a fight against Byleth in the original timeline, but survives in this one thanks to Arval's intervention. Shez ends up replacing Byleth as the one who saves Edelgard, Dimitri, and Claude from Kostas and his bandits, essentially taking their place in the narrative — albeit as a student at Garreg Mach rather than a teacher — with Byleth remaining a mercenary themselves under Jeralt that inevitably ends up hired by whichever faction Shez has to fight against.
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 Fire Emblem Warriors: Three Hopes (Video Game)
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The big reveal in Kingdom Hearts: Birth by Sleep is that Terra, one of the main protagonists, eventually gets his body hijacked by Master Xehanort, the main antagonist. As Terra-Xehanort, he releases his heart and gives birth to Ansem, Seeker of Darkness, the antagonist of the first game, and Xemnas, the antagonist of II.
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 Kingdom Hearts: Birth by Sleep (Video Game)
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In Hand of Fate 2, though with a bit of a twist: the first game makes it clear that Kallas, the player character, was always a cruel and violent person, so when you face him as the final boss in the sequel, it's not entirely out of the blue.
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 Hand of Fate (Video Game)
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Rogue Protagonist
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TRON: Clu has a small role in the original film as one of the hero's programs. In TRON: Legacy, his upgraded version is the main villain. Also, Tron has been brainwashed into "Rinzler", Clu's chief thug.
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 TRON
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Aqualad in Young Justice (2010). After spending the first season as the Arc Hero, he's become The Dragon in the second. While ultimately revealed to be a Fake Defector sent by Nightwing to infiltrate The Light, he is forced to commit genuinely villainous acts to maintain his cover.
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 Young Justice (2010)
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If we look at the series' timeline, Naked Snake/Big Boss is one. He's the hero in Metal Gear Solid 3: Snake Eater, Metal Gear Solid: Portable Ops, Metal Gear Solid: Peace Walker, Metal Gear Solid V: Ground Zeroes and Metal Gear Solid V: The Phantom Pain, and the Big Bad of Metal Gear and Metal Gear 2: Solid Snake. And reappears in Metal Gear Solid 4: Guns of the Patriots's epilogue to tie up the loose ends.
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 Metal Gear Solid 3: Snake Eater (Video Game)
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Lucian the divine is the canon name of the protagonist of Divine Divinity, and he does this twice:
First in Divinity II: The Dragon Knight Saga, Lucian is the Final Boss of the normal route.
Before Divinity II (Canonically) in Divinity: Original Sin II, Lucian turns out to be The Man Behind the Man of Magister Dallis, who is working towards the same goals as her. Sure enough, Lucian is one of the final bosses of Original Sin II, though not the TRUE Final Boss (that honour goes to Braccus Rex, who is the only one who must be defeated.)
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 Divine Divinity (Video Game)
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Rogue Protagonist
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In Scooby-Doo (2002), it turns out that the main villain is actually a disguised Scrappy-Doo, who was booted out of Mystery Inc. prior to the events of the movie.
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 Scooby-Doo (2002)
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Caim, the protagonist of Drakengard, appears about halfway through the sequel as the "One-Eyed Man" responsible for the death of Nowe's adoptive father. He's basically the same person he was in the first game. He's just not the viewpoint character anymore.
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The protagonist of the original Japan-only King's Field game was Prince Alfred. In the third game (King's Field 2 in international releases), King Alfred has been possessed by the Big Bad, and his son Prince Lyle must confront him to save the kingdom.
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This seems to be the trend in the NecroVisioN series. The protagonist of the prequel ends up becoming the Disc-One Final Boss of the main game, while the protagonist of the main game either becomes the Devil's right-hand General or (in the hardest to obtain ending) ends up becoming the Lord of Hell himself. In either case, it's pretty clear he'd be the Big Bad if any sequel was ever made. In both cases, they turned to the dark side with the intention of preventing a greater evil from occurring.
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This happens quite a lot in the Contra series.
The most notable examples are Contra: Shattered Soldier and its sequel Neo Contra. In Shattered Soldier it's revealed that the terrorist leader and Disc-One Final Boss is in fact Lance Bean, Player 2 of the classic Contra series, who as it turns out is a Well-Intentioned Extremist trying to stop the World Government from destroying the planet, but who was driven insane by the Red Falcon cell he injected into himself to survive an early assassination attempt by the World Government. In Neo Contra, Bill Rizer (Player 1 of the classic series and Shattered Soldier) is the Big Bad and final boss, who wants to destroy the Earth For the Evulz (although it's heavily implied that he's actually an insane A.I. based off of Bill's mind, with the real Bill Rizer being the mentor character). Lucia (Player 2 of Shattered Soldier) is also a member of the Quirky Miniboss Squad and seems gleefully evil in helping Bill destroy the world. Unlike Lance, she dies without any explanation being given for her abrupt Face–Heel Turn.
Also happens retroactively in Hard Corps: Uprising, where the main character is a young Colonel Bahamut, who was the Big Bad of the original Contra: Hard Corps.
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J.C. Denton, the protagonist of Deus Ex, becomes one of the major faction leaders in the sequel, Deus Ex: Invisible War, and is also arguably the character who is most centrally driving the game's plot (a role that usually falls to the Big Bad). You can join his faction in one ending path (and the majority of the game's plot seems to be building up to this), but if you chose any of the other 3 ending paths, he becomes the "final boss" of the game, since assassinating him becomes one of the key endgame objectives. Denton has changed quite a bit between the two games, but can still arguably be described as a "good guy", and Invisible War is much more Gray-and-Gray Morality than the first game.
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Rogue Protagonist
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In Gothic 4, the Evil Overlord Big Bad is King Rhobar III, aka the Nameless Hero, the protagonist of the previous three games. It turns out he's possessed by a demon lord, though, and he gets exorcised in the ending.
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The father from Lakeview Cabin becomes one of the killers on the loose in the third episode of Lakeview Cabin Collection along with his son.
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In Armored Core: For Answer, main character from Armored Core 4 is the pilot of White Glint, with Fiona still being his operator, who have since joined Line Ark after Anatolia got destroyed at the end of 4. You either fight them or side with them; either way, Anatolia's Mercenary gets downed defending Line Ark.
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 Armored Core: For Answer (Video Game)
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Richter Belmont was the main character of Castlevania: Rondo of Blood. Five years later for Castlevania: Symphony of the Night, Dracula's castle is back, with Richter in charge. In truth, he was manipulated by the magic of the dark priest Shaft.
 Rogue Protagonist / int_d5f41057
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 Castlevania: Rondo of Blood (Video Game)
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It's implied in Armored Core 2 that Leos Klein is the player raven from Armored Core: Master of Arena and the original Ninebreaker.
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 Armored Core 2 (Video Game)
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Also happens retroactively in Hard Corps: Uprising, where the main character is a young Colonel Bahamut, who was the Big Bad of the original Contra: Hard Corps.
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 Hard Corps: Uprising (Video Game)
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Another protagonist gone rogue from Birth by Sleep is Aqua, who in III succumbs to darkness and has to be fought as a boss. For an added emphasis, you are playing as Sora, who can be considered as her successor in-story. It doesn't last long, however.
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 Kingdom Hearts III (Video Game)
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After being the chief Kaiju hero of Godzilla (2014), and especially Godzilla: King of the Monsters (2019) where he's at his most heroic while saving the world from King Ghidorah, Godzilla seemingly becomes a hostile antagonist in Godzilla vs. Kong; attacking populated manmade structures for mysterious reasons, and driving Team Kong to try and reach the Hollow Earth in the hopes they can use its Unobtainium to neutralize him. Between the film's two titular kaiju, Kong is the more protagonistic and virtuous-seeming of the two, while Godzilla is portrayed as an obstacle in Kong's plot. Subverted when it's revealed that Godzilla is specifically attacking Apex facilities because he can sense that their experiments are reanimating Ghidorah's remains, and Apex have been actively taking advantage of this to frame Godzilla as a rabid menace; making Godzilla's ruthless measures against the humans whom are in his way very understandable, after everything him and humanity did side-by-side to stop Ghidorah exterminating everyone in the previous film. It culminates in Godzilla and Kong working together to destroy Mechagodzilla after Ghidorah's subconsciousness has possessed it.
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In UQ Holder!, the Stealth Sequel to Negima! Magister Negi Magi, it's ultimately revealed that Negi Springfield defeated the Mage of the Beginning 20 years earlier, and ended by being possessed by her. As a result, Touta and the rest are forced to fight a Brainwashed and Crazy Negi.
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Dead Rising:
In Dead Rising 2: Off the Record, Chuck Greene appears as a Psychopath, having failed to save Katey in this continuity. Similarly, Stacey is the Big Bad of the game, replacing Sullivan.
The Stinger of Dead Rising 3 reveals that Isabella Keyes has developed a hatred for America that surpasses her brother's.
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 Dead Rising (Franchise)
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R.O.D the TV begins with new characters who weren't in the OVA. When the original cast shows up, they're no longer on the same side, and one of them is the Big Bad.
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The final season of Shakugan no Shana opens with Yuji's apparent death... only for him to turn up as leader of the bad guys.
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Armored Core:
It's implied in Armored Core 2 that Leos Klein is the player raven from Armored Core: Master of Arena and the original Ninebreaker.
In Armored Core: For Answer, main character from Armored Core 4 is the pilot of White Glint, with Fiona still being his operator, who have since joined Line Ark after Anatolia got destroyed at the end of 4. You either fight them or side with them; either way, Anatolia's Mercenary gets downed defending Line Ark.
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 Armored Core (Video Game)
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Super Joe was the main protagonist of the original Bionic Commando (1987) and was also the player character of many other Capcom games from the 1980s and 1990s. In the 2009 Bionic Commando game, however, he's the Big Bad.
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In Scott Pilgrim Takes Off, we are introduced to Older Scott, two versions of the title character that had gone through the same events as the original comic and actually got to marry Ramona. But a string of poor communication causes the two to split up, which embitters Older Scott to the point of a Face–Heel Turn. This makes Older Scott go back to the past to capture Scott and prevent him from fighting the evil exes so he doesn't go through the hardships he did when falling out with his wife.
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In Torchlight II, the Alchemist, one of the three player classes of the first game, is revealed to still have the Ember Corruption, and has become obsessed with it. By the time the story starts, he's murdered Syl, blown up Torchlight, and stolen the Heart of Ordrak, the first game's Big Bad.
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Vito Scaletta, the protagonist of Mafia II, appears in Mafia III as an ally of that game's protagonist, Lincoln Clay. If Clay doesn't give Scaletta a fair amount of rackets and territories, the latter will betray the former and will have to be fought and killed.
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 Mafia II (Video Game)
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Rogue Protagonist
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In Dead Rising 2: Off the Record, Chuck Greene appears as a Psychopath, having failed to save Katey in this continuity. Similarly, Stacey is the Big Bad of the game, replacing Sullivan.
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1.0
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 Dead Rising 2: Off the Record (Video Game)
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Kingdom Hearts:
The big reveal in Kingdom Hearts: Birth by Sleep is that Terra, one of the main protagonists, eventually gets his body hijacked by Master Xehanort, the main antagonist. As Terra-Xehanort, he releases his heart and gives birth to Ansem, Seeker of Darkness, the antagonist of the first game, and Xemnas, the antagonist of II.
Another protagonist gone rogue from Birth by Sleep is Aqua, who in III succumbs to darkness and has to be fought as a boss. For an added emphasis, you are playing as Sora, who can be considered as her successor in-story. It doesn't last long, however.
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 Kingdom Hearts (Franchise)
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During Part III of Fire Emblem: Radiant Dawn, Ike, protagonist of the previous game Path of Radiance, and Micaiah, the protagonist during Part I of Radiant Dawn, end up commanding opposing armies and clash several times, with the player switching perspectives between chapters. Ike is the boss of Chapter 3-13 and Micaiah is the boss of Chapter 3-Endgame, though both chapters can be completed without ever attacking them (and the story doesn't change even if you do).
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 Fire Emblem: Radiant Dawn (Video Game)
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comment
Kamen Rider Decade plays with this, as Tsukasa/Decade spends Final Chapter hunting down all the Kamen Riders, while the Riders believe that they must stop Decade's rampage in order to save The Multiverse. In the end, Decade turned out to still be Good All Along, as his trying to "kill" the Riders note actually preserving them in cards was the only way to save the Multiverse and the Kamen Rider legacy.
In general, this plot tends to happen a lot in tokusatsu crossovers, with one set of heroes believing the other to be villains until they eventually discover the truth. Some examples include Gekisou Sentai Carranger vs. Ohranger (in which the monster tricks the Carrangers into taking his side against the Ohrangers), Gokaiger Goseiger Super Sentai 199 Hero Great Battle (in which the Goseigers and Gokaigers come into conflict over possession of the Goseiger Ranger Keys), Tokumei Sentai Go-Busters vs. Kaizoku Sentai Gokaiger: The Movie ( in which the Gokaigers work for Zangyack while trying to undermine them from inside), and Kamen Rider X Super Sentai Superhero Taisen (in which Tsukasa and Marvelous only pretended to kill the other heroes to lure out the villains).
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In The Fate of the Furious, Dom seemingly turns to the dark side courtesy of the Big Bad, Cipher. His own team has to try and hunt him down to get some answers. Cipher's blackmailing him with the lives of his ex-lover and baby son.
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Star Trek: The Next Generation:
Picard is assimilated into the Borg Collective in "The Best of Both Worlds". Slightly averted in that he did not join willingly and was thus forcibly integrated into the collective consciousness, but from the point of view of Starfleet played terrifyingly straight, as the Borg gained knowledge of high-level Starfleet tactics and used that knowledge to great effect at Wolf 359.
Subverted in "Unification, Part 1"/"Part 2". When Spock goes to Romulus, Starfleet Command is worried that he has defected. It turns out that his motives are entirely heroic.
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The following is a list of statements referring to the current page from other pages.

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Heel/Face Index
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Villains
 Batman Vampire (Comic Book) / int_3c75b649
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 Elementals of Harmony / Fan Fic / int_3c75b649
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Rogue Protagonist
 The Immortal Game / Fan Fic / int_3c75b649
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Rogue Protagonist
 Chika's Bizarre Adventure (Fanfic) / int_3c75b649
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Rogue Protagonist
 ElementalsofHarmony
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 Prefects Before Dawn (Fanfic) / int_3c75b649
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 The Rival Prefects Trilogy (Fanfic) / int_3c75b649
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Rogue Protagonist
 Captain America: Civil War / int_3c75b649
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 Red Country / int_3c75b649
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 AirshipCanon
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Rogue Protagonist
 DarkerThanBlackTwinsOfTheMeteor
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Rogue Protagonist
 Looney Tunes Collector Martian Alert
seeAlso
Rogue Protagonist
 TalesOfSymphoniaDawnOfTheNewWorld
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Rogue Protagonist
 Saki Achiga-hen (Manga) / int_3c75b649
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 Class Trials Season 1 (Roleplay) / int_3c75b649
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 Class Trials Season 2 (Roleplay) / int_3c75b649
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Rogue Protagonist
 Kamen Rider Decade / int_3c75b649
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 Armored Core (Video Game) / int_3c75b649
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 Armored Core 2 (Video Game) / int_3c75b649
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 Beyond Good & Evil 2 (Video Game) / int_3c75b649
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 Bionic Commando (Video Game) / int_3c75b649
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 Call of Duty: Modern Warfare II (Video Game) / int_3c75b649
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 Culdcept (Video Game) / int_3c75b649
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 Diablo II (Video Game) / int_3c75b649
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 Divinity: Original Sin II (Video Game) / int_3c75b649
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 Drakengard (Video Game) / int_3c75b649
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 Far Cry 2 (Video Game) / int_3c75b649
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 Fire Emblem Warriors: Three Hopes (Video Game) / int_3c75b649
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 Five Nights at Freddy's World (Video Game) / int_3c75b649
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 Gal Guardians: Demon Purge (Video Game) / int_3c75b649
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 Gothic (Video Game) / int_3c75b649
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 In Stars And Time (Video Game) / int_3c75b649
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 JOLLY (Video Game) / int_3c75b649
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 Kingdom Hearts: Birth by Sleep (Video Game) / int_3c75b649
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 Kingdom Hearts III (Video Game) / int_3c75b649
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 King's Field (Video Game) / int_3c75b649
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 KISS: Psycho Circus: The Nightmare Child (Video Game) / int_3c75b649
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 Legacy of Kain: Soul Reaver (Video Game) / int_3c75b649
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 Madagascar (Video Game) / int_3c75b649
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 Mafia III (Video Game) / int_3c75b649
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 Mogeko Castle (Video Game) / int_3c75b649
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 Paint the Town Red (Video Game) / int_3c75b649
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 Phoenix Wright: Ace Attorney: Conflict of Interest (Video Game) / int_3c75b649
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 Resident Evil 5 (Video Game) / int_3c75b649
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 S.T.A.L.K.E.R. (Video Game) / int_3c75b649
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 Silent Scope (Video Game) / int_3c75b649
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 Slender: The Arrival (Video Game) / int_3c75b649
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 South Park: The Fractured but Whole (Video Game) / int_3c75b649
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 Spark the Electric Jester 3 (Video Game) / int_3c75b649
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 Tactics Ogre (Video Game) / int_3c75b649
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 Tales of Symphonia: Dawn of the New World (Video Game) / int_3c75b649
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 The Trapped Trilogy (Video Game) / int_3c75b649
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 Torchlight II (Video Game) / int_3c75b649
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 Touhou Mother (Video Game) / int_3c75b649
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 White Dwarf (Video Game) / int_3c75b649
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 eXceed / Videogame / int_3c75b649
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 Hand of Fate (Video Game) / int_3c75b649
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 Where Was My Hero...? (Web Animation) / int_3c75b649
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 Monster Factory (Web Video) / int_3c75b649
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 Real-Time Fandub (Web Video) / int_3c75b649
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 Darths & Droids (Webcomic) / int_3c75b649
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 Pokequest (Webcomic) / int_3c75b649
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 The LEGO Movie 2: The Second Part / int_3c75b649
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 The Killer Rarityverse (Fanfic) / int_3c75b649
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 [PROTOTYPE 2] (Video Game) / int_3c75b649
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