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Anime and Manga
- 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.
- 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, has been plotting doomsday for quite a while, and, in fact, sucessfully 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.
- Kamikaze Kaitou Jeanne, Finn has been using them, and the rival angel is trying to stop Finn as he knows that she has been possessed by evil.
- In Darker Than Black, The Syndicate has been plotting for years to annihilate all Contractors, which Evening Primrose, 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, essentially making the majority of the cast bad guys.
- 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.
- 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.
Film - Animation
- 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.
Film - Live Action
- 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).
- 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.
- 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.
- 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.
- 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.
- This is the twist in The Sword of Good. The "good guys" are actually agents of 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.
Live Action TV
- 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.
- 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.
- 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.
- 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.
- 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.
- In Tales of Phantasia, the villain is basically trying to save his people, and create a mana seed. In fact, he helps restore mana, since humans and half-elves have been using it up. Cless, Chester, and the rest are not exactly villains, but they are on the wrong side, as a result of only understanding the problem from a human point of view.
- It doesn't help that the villain never explained his intentions. Instead of trying to reason with humanity, explaining that their actions were harming the Mana Tree (which would also cause problems for them), he went straight to declaring war and trying to destroy everything in his way. The protagonists, and thus, the players, only discover his goals at the very end - even then, it was a different character doing the exposition.
- Altair spends most of Assassin's Creed I 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.
- 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.
- 1: 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.
- 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.
- 3: The pirates and privateers that control the North and South Rook Islands are run by a psychopath and a sociopath. You kill them to free Rook and allow your faction to take over. Then your faction's leader tries to force you into killing your friends. If you do as she says, she'll end up backstabbing you so that she can have unquestioned worship from both islands.
- 4: This game is the one that focuses on Wrong Side All Along: Pagan Min, the "King of Kyrat", is a psychopathic dictator whose primary source of income is the drug trade - and secondary source being slave labor. He has set up a cult of personality and orders the slaughter of entire towns for not perpetrating constant worship (or at least lip service). And he occasionally goes out into the wilderness and shoots up citizens and endangered species for kicks (Some people pay Pagan Min $200,000 to hunt a rhino). Unfortunately, each of the three possible leaders that can destroy his regime and take over will end up exaggerating one of these three properties to a logical extreme. If Amita takes over, she will turn Kyrat into a Drug-Communist state: she will end up forcing children to fight trained armies, increase the size of the local opium fields and their slave workers, and possibly kill an eight-year old kid, Bahdra, whose only crime was being declared the girl-pope. If Sabal takes over, he will turn Kyrat into a militant Theocracy: he will repress Kyrat's progress, declare Bahdra a goddess, and kill anyone who refused to worship his religion (or even paid lip service to another religion) for the past twenty years - which, considering Pagan Min's cult of personality ran for over twenty-five, is a fucking lot. If Ajay (the player character) takes over, he will prove himself a decent ruler, but a horrible sociopath: killing random bystanders and slaughtering entire species for fun and profit. Note that Ajay can choose if Amita or Sabal takes over, and then kill them and take over himself if he's horrified at what they do to Kyrat. And then he can choose whether or not he wants to stay and keep pointlessly fighting or leave the country to its fate. And as some kind of insult, we find out that Mohan "Hero of Kyrat" Ghale is partly responsible for Kyrat's suffering - his wife fell in love with Pagan Min, and she almost reformed him, but after years of betrayal and failure as a king on Pagan's part Mohan snapped, stormed the palace like a badass, and killed their love-child daughter. The end result was that a true warrior was responsible for Pagan Min's insanity and the country's downfall. The whole game is a jab at politics, where just because you fight hard and fight fair doesn't mean you're in the right, or fighting for the right people, or even should fight when you could do better by playing the diplomatic route (if you refuse to fight or even move at the beginning of the game, Pagan Min declares Ajay his heir). Emphasis on 'could', though.
- 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.
- In Bravely Default, Eternia and its Jobmasters 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. It turns out, Airy is in fact The Dragon and by Awakening the Crystals, the party is further destabilizing all the different Luxendarcs. 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 the true Big Bad.
- 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.
- Happened to Schlock's mother in Schlock Mercenary. Schlock's human grandmother was a slave trader and she 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.
- Starwalker: Starwalker and her crew find out that the person who hired the Space Pirates was the avatar of our sun who didn't like be 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.