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Wrong Side All Along
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 redeem them. 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.

Because of the nature of this trope, there will be spoilers.

Examples:

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 Rebellious 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.

Comics
  • 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
  • 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, 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.

Literature
  • 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.

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.

Video Games
  • 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.

Web Original
  • 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.

Police Brutality GambitBetrayal TropesYou Said You Would Let Them Go
The Wicked StagePages Needing WicksYou Make Me Sick
Would Not Shoot a Good GuyExample as a ThesisYou Are Already Checked In

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