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Anime and Manga
- In Fullmetal Alchemist, all the military operations of the Amestrian Military were orchestrated to sacrifice the entire country to make a massive Philosopher's Stone, so that Father could absorb Truth, i.e. Fullmetal Alchemist's god.
- In the 2003 anime version, the plan is instead for the Homunculi to use the country to make Philosopher's Stones and become human.
- Except the Homunculi were also being used all along, and Dante didn't really care for turning them into humans at all, she just needed the stone to mantain her imortality.
- In the 2003 anime version, the plan is instead for the Homunculi to use the country to make Philosopher's Stones and become human.
- Magic Knight Rayearth. Emeraude summons the Magic Knights to Cephiro to kill her.
- Maybe Gendo Ikari, who might be on the Grey side of the Black and Very Dark Grey Morality, and definitely Keel Lorenz from Neon Genesis Evangelion.
- Oban Star Racers, in which, yup, the whole thing is an Evil Plan (more like a Gambit Roulette really) by the Big Bad, Canaletto.
- In Superman & Batman: Generations, Bruce Wayne Junior as Batman investigates Ra's Al Ghul's organization, and when confronting the head finds out it's not Ra's but Bruce Senior, who beat Ra's once and for all ten years before and has found a way to overcome the Lazarus Pit's limitations. He has turned the organization to the good while maintaining a criminal front. He then makes Junior its new CEO, and resumes his life as the Batman.
- The entire rationale behind With Strings Attached is that the four are being used by the Fans. First they're sent to C'hou by Shag and Varx as part of an undergraduate Alien Psychology experiment. After this collapses and things go weird, they're sent on a quest to remove a curse from a continent and told that's why they were sent to C'hou in the first place. Everyone thinks the C'hovite gods set them on the quest path, but it was actually engineered by Jeft. They mostly learn the truth about Jeft's manipulations, but they never do learn about those of Shag and Varx, because the two lie quite convincingly to the four.
Films — Animated
- The Man Called Flintstone: Fred finds out that The Green Goose, nefarious James Bond villain he's been after is actually Agent XXX (not to be confused with Vin Diesel or Ice Cube).
Films — Live-Action
- In Death Wish 4: The Crackdown, Kersey finds out the rich man who offered him assistance to take out the drug dealers, wasn't a corporate executive, the person he impersonated was out of the country for several months, the man he dealt with was really the rival of the other dealers, and was basically using Kersey to eliminate the competition. Please note that this plot twist appeared earlier in The Saint in New York and The Saint Meets a Phantom.
- As Jack is bargaining with Barbossa for Will's life in the fantasy film Pirates of the Caribbean: The Curse of the Black Pearl, and to destroy the men of the Dauntless (more or less), plus getting to sail the Pearl again as captain, Will bursts out "You've been planning this from the beginning!"
- Season of the Witch actually is about this sort of plot— the Big Bad tricked not only the main character, but the entire branch of the Catholic Church backing an expedition to remove her power and its effects by taking her to an ancient monastery where a ritual can be performed to do so. Unbeknownst to them, the monks are all dead and the monastery desecrated, and the demon actually wanted to be taken there so that the usual restrictions against demons entering churches didn't apply, and she could use the particular book of rituals to destroy humanity.
- In doing this, she even makes them think they've figured out her tricks (and made the audience think she was entirely ineffectual) in her obvious displays of witchcraft while she was talking about being innocent. When all along, she wanted them to think her guilty.
- This is the surprise twist in the thriller State of Play. Critics generally called it a Shocking Swerve.
- The original Total Recall (1990) uses this, with the added twist that the villain who set the plot is the protagonist himself (via Memory Gambit).
- Played with in The First Law; the revelation is that Bayaz is actually a villain, but he doesn't hide the fact that the MacGuffin he's after- the Seed- is a terrible destructive weapon, and the enemies he plans on using it on really are as insane and dangerous as they appear to be and need to be stopped, even if Bayaz is probably more evil. Plus, the quest to find it fails (though it turned out to be closer than anyone thought), and the Ragtag Bunch of Misfits he assembles aren't actually very nice people. Ferro, the one who actually finds the Seed, discovers what a treacherous backstabbing bastard Bayaz is as soon as she gets it...but decides to let him have it anyway, since they happen to have the same enemies and she hates them even more than he does. Ferro regrets it, but that regret becomes an Ignored Epiphany.
- Done twice in fact, when its discovered that Quai- Bayaz's assistant- was murdered and replaced by Tolomei, a girl from Bayaz's past he claims was killed by her father (when in fact he murdered both of them). Played more straight in that she wants it to bring forth The Legions of Hell and bring about The End of the World as We Know It, and nobody thinks thats a good idea.
- In The Man Who Was Thursday, Sunday does this to the entire police force/anarchy council. Unusually in this case, Sunday is a good guy, using other good guys.
- In the Memory, Sorrow and Thorn series by Tad Williams, it is revealed at the end that the titular three magic swords that the heroes were gathering to stop Ineluki were actually the three talismans necessary to free Ineluki. What makes this especially appalling is that the heroes found out about the swords in the first place from a mystical dream, but they also knew that mystical dreams were under the control of Ineluki.
Live Action TV
- Sloan and SD-6 on Alias, though unusually, it is revealed almost immediately.
- In CSI, we're led to believe season 8's Big Bad is Lou Gedda, until the finale when Undersheriff McKeen shows his True Colors by murdering Warrick.
- Doctor Who and the entire 16th season, also known as The Key to Time, where the White Guardian asks the Doctor to find the six segments of the Key to Time, because the Black Guardian is planning to unravel the universe with it. Well, the White Guardian was the Black Guardian all along...
- Every Winchester in Supernatural falls into this trope, due to the plot formulated by Lucifer and Azazel over 20 years ago. Especially John and Dean, but especially especially Sam. Several people use this as evidence that there is no free will- or at very least, not for humans.
- In the seventh season of 24 Tony turns out to be playing everyone at the end of the season. Him warning Jack, Chloe, and the FBI about an attack and Washington D.C. and working with them to stop it was all to obtain a bio-engineered virus that the terrorist cell he was working with wanted obtain, but then it turns out at the very end that he was doing that for them all to get in good graces with and meet their ringleader so he could kill him since said ringleader had masterminded the death of his pregnant wife.
- Call of Cthulhu supplement Curse of the Chthonians, adventure "The Curse of Chaugnar Faugn". The investigators are manipulated into helping a mad professor bring the statue of a powerful Mythos deity to life.
- Dungeons & Dragons adventure The Apocalypse Stone. A high level wizard tricks a party of PC's into stealing a stealing a powerful magic item for him by pretending to be a divine messenger.
- The calling card of any plot by the Eldar, Tzeentchians, and the Deceiver in Warhammer 40K.
- Assassin's Creed I: All of the assassinations Al Mualim had you were performing were done so he would be the only one with knowledge and possession of the Piece of Eden. He's also the tenth Templar. Magnificent Bastard indeed. Oh and Nice Job Breaking It, Hero.
- The true Big Bad Juno used everyone, Assassins and Templars alike, throughout the entire series to escape her prison and give her another chance to rule humanity. The Hero learns this only after he has no choice but to go along with the villain's plan, since the alternative is letting the world be burned by a solar flare. Twisting the knife even further, the method he uses to save the world and free Juno also kills him so he won't be around to oppose her.
- Baten Kaitos, specifically the second game of the series. You work for the person who is THE Magnificent Bastard of the entire game, although he stealthed his way out of being seen as one.
- BioShock: You've been bioengineered, programmed, mailed to the outside world and called back to Rapture all so Frank Fontaine could use you to take over the city- given that you're the only other person in Rapture who can use the Vita-Chambers and fog the security systems. And who is Fontaine? Why he's the friendly Irish rebel who's been helping you for most of the game!
- Bomberman 64 Sirius, it turns out, is using you to get to Altair.
- Castlevania: Order of Ecclesia did this. Just saying the title's probably spoiling it, as there's really only one person who you report to in this game.
- Code Name: Viper has the player rescuing fellow operatives, each of whom has bits and pieces of a message revealing the identity of the terrorist leader. It turns out to be the general Viper was working for, making him the last boss fight.
- Crackdown: The Agency turns out to be one of these.
- The original Metal Gear: Big Boss is the Big Bad! In Metal Gear Solid Snake's entire mission is to activate REX for Liquid.
- Deus Ex: JC's employer for the first three missions is a corrupt transhumanist whom JC then fights.
- The entire quest-line involving the Black Soulstone from Diablo III, which takes up the majority of the second and third acts and involves the killing of the final two Great Evils...so that Adria, who it turns out is a servant of Diablo, can use it to resurrect her master as the embodiment of all seven Great Evils in one being, in accordance with his centuries-in-the-making Evil Plan to destroy the High Heavens and end the war between Heaven and Hell once and for all.
- The storyline of Double Dragon III, when the Lee brothers help an old person who was Evil All Along.
- Dragon Age: Inquisition the ending reveals that Solas was using everyone for his own means the whole time - both the Inquisition and the Big Bad of the game.
- Final Fantasy XIII: All of the fal'Cie are driving the heroes to destroy Cocoon. ALL OF THEM.
- God of War III does this twice. First, the Narrator of the first two games turns out to be Gaia, a Titan who was using Kratos in the their war against Zeus. She decides to betray and leave him for dead at the beginning of the game. Then during the climax, it's revealed that Athena was using Kratos to overthrow both Aries and Zeus so that she could rule uncontested. Zeus believed that Kratos fulfilled the prophecy of one of his children betraying him, but it was Athena who was the betrayer all along. Kratos was set off by her actions.
- The final boss of Milky Way Wishes in Kirby Super Star: Marx, who asked you to summon the wish-granting comet Nova so he could wish to control Popstar.
- Again in Kirbys Return To Dreamland: Magolor manipulated Kirby and his friends into rebuilding the Lor Starcutter and fighting Landia in order to steal the wish-granting Master Crown.
- Jade Empire: Taken to it's logical extreme. Your master, who raised you from a child, trained you as part of an elaborate plot to kill the current Emperor. He planned everything perfectly so that you would think you are merely saving your master when instead you are clearing the way for him to become Emperor. Glorious Strategist indeed!
- In Mega Man X: Command Mission, Colonel Redips, both as himself and party member Spider, commands X and Zero to take out Epsilon's Rebellion Army so he can get their Supra-Force Metal for himself.
- This is the storyline of Konquest mode of Mortal Kombat: Deception.
- In Rune Factory, the Laser-Guided Amnesia protagonist was put there as a deliberate plot to awaken Terrable-a powerful dragon. All goes nicely according to plan until Terrable is defeated and later disables the attacking 100 tanks.
- One of the storylines in Sonic Heroes involves someone hiring the protagonists to solve a crime. This person turns out to be Eggman. Subverted though, he really did need their help.
- Strife: Macil apparently sent you after the pieces of the Sigil to acquire the complete artifact and free the One God, though he was obviously insane and possessed by a Spectre, so he might have originally had honest intentions before he got possessed. And the Oracle (in the "bad" story branch) does the same thing, sending you after the Sigil pieces and finally mocking you for falling for its ruse. In the bad ending, it's also strongly implied that your Mission Control, Blackbird, was actually the Entity manipulating you into acquiring the Sigil and using it to free the Entity.
- System Shock 2: Dr Janice Polito had an agenda - or more accurately, SHODAN did. Every one of her interactions with you is designed to make you forget what threat she poses, then, once you give her what she needs, You Have Outlived Your Usefulness.
- Wario Land 3: "A hidden figure" is actually Rudy the giant evil clown, taking advantage of Wario's greed in order to unseal himself.
- WET's first mission has Rubi retrieving a stolen heart that is needed for the father of her client Trevor Ackers. One year later, Trevor's father, William Ackers, hires her to bring Trevor back from Hong Kong because he doesn't want his son mixed up in the criminal element. Only when she brings him back, William then proceeds to have Trevor's head chopped off, then leaves Rubi to die at the hands of Ze Kollecktor. Turns out that the man who Rubi got the heart for and the person who hired her for the second job weren't the same person. Kidnapping Trevor was a set up for Rubi so that Rupert Pelham could eliminate the Syndicate and it's monopoly on the Asian Drug Market.
- K.O.L.M.: In both games, though clearer in the second game where you have a definite goal: reunite Sis with Father. Turns out it was so he could forcibly turn her into a robot.