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Anime And Manga
- The Big Bad of Naruto has, at various points, been: Orochimaru (former Akatsuki member) -> Akatsuki itself (Itachi being its most visible player) -> Pain -> Tobi and Danzo -> Kabuto and Tobi combined -> Madara & Obito with Orochimaru on the fringes -> Madara after throwing Obito away -> Kaguya after stabbing Madara -> Sasuke after helping Naruto seal Kaguya -> Toneri when he tries to crash the Moon into the Earth -> Momoshiki Otsutsuki, who is Kaguya's rival in monopolizing chakra.
- In Fairy Tail, Jellal starts out as the apparent Big Bad of the series. Then it turns out he's being manipulated by his right-hand woman Ultear, who is actually The Dragon to Hades. When Hades steps in as the Big Bad, he wants to get Zeref to become the Big Bad. Then it turns out Zeref was always the Big Bad, but he just didn't feel like doing anything until this point. He's challenged by two other powerful enemies: Acnologia, whom he wants to kill; and E.N.D., whom he wants to be killed by.
- Mystique and Bolivar Trask compete for title of villain in X-Men: Days of Future Past; it's Trask's Sentinels that lead to the Bad Future, but it's Mystique killing him and being captured for experimentation that leads to the Sentinels getting approved by the government, making her the one whose Evil Plan needs to be stopped. Additionally in the future Trask and Mystique are dead, making it the Sentinels themselves that are the villains. And then in the past Magneto ends up becoming a third villain when he decides to kill Trask and the President.
- A Song of Ice and Fire: Good luck guessing who is ultimately behind any given act of villainy.
- So, in the Molly Moon series, there's Primo Cell, who's really being controlled by Lucy Logan, the librarian. But then we learn that the real person with the strings is Cornelius Logan, crossdressing as his sister Lucy. Okay... And then in the third book, it turns out Waqt hypnotised Cornelius into his Start of Darkness. Wow.
- Hoo boy, The Chathrand Voyages, which could just as easily be called "Gambit Pileup- The Epic Fantasy", despite the action largely being confined to the eponymous ship. Let's take a look, shall we?
- Sandor Ott wants to start a civil war in the Mzithrin Empire by freeing the Mzithrini tyrant and war-criminal the Shaggat Ness and returning him to his followers.
- Arunis tricked Ott into thinking it was a good idea as part of stage one of a plan to recover the Shaggat's Artifact of Doom and destroy the world.
- His on and off co-conspirator and rival and sister Macadra wants the same artifact and sent him to get it, but she wants to rule the world rather than destroy it.
- The Shaggat himself thinks fate is manipulating all of them to help him fulfil his destiny as a Dark Messiah.
- Master Mugstur is the psychotic, sentient rat who wants to take over the ship at the head of an army of regular rats because he thinks Rin wants him to (and eat the Captain's tongue while he's at it).
- Lord Talag is the eight-inch-high Chessmaster who wants to use the Chathrand to find his people's lost homeland, then scuttle it there and kill everyone aboard except his followers. He's aided and abetted by his son Taliktrum, who starts plans of his own that quickly spiral out of control.
- The Swarm of Night is the entity Arunis ultimately intends to summon. It doesn't really make anything that can rightly be called "plans" of its own, but the threat it offers to the world is greater than all of the above combined and by the end of the third book, it's loose.
- Needless to say, they all trip over each other at every turn. Yikes.
- Warrior Cats descends into this in the Dark Forest storyline. Every major villain in the series, and a few new ones, team up to destroy the Clans. The story leads us to think that Tigerstar, Hawkfrost, Brokenstar, or Mapleshade is the villain, without ever giving a definitive answer on who's behind it all. Even Ivypool is confused, and the information she relays to the other characters reflects it. Not that this is a bad thing.
- Very much so in Warrior Cats: Dawn of the Clans . The first novel sets up Clear Sky as a villain. This continues throughout the second and third novel. However, Clear Sky regrets his actions and tries to makes up for them. The fourth book introduces One-Eye and Star Flower as villains, with the former dying that very book. In the fifth book, we are introduced to Slash, and the story makes Star Flower's choice of side unclear. By the last book, Slash is the final boss, and Star Flower is good.
- The Death Gate Cycle begins with one Big Bad, Lord Xar (though the main character is his Dragon), but as it goes on picks up more main villains with increasingly complicated relationships. The necromancer Kleitus is the ruler of the lazar and despises all life and seeks its destruction; when Xar encounters Kleitus he manages to defeat him and force him into servitude, but Kleitus hangs around mostly for the chance to kill Xar while his back is turned while trying to manipulate him for his own ends. The Serpents are a timeless force of evil who feed off chaos and negative emotions, and willingly subordinate themselves to Xar in the hopes of manipulating him into causing unprecedented destruction - their leader is the Royal One, but he rarely shows up and plays little direct role, leaving the position of The Heavy and The Face of Serpents as a faction to Sang-drax. Sang-drax and Kleitus don't get along and are seen to try and manipulate Xar in opposite directions, while Xar himself trusts neither of them and generally does what they want only insofar as its suits his goals. Then there is Samah (who is replaced by his son Ramu after he dies) who opposes Xar and is also working with the Serpents, who like to play both sides wherever possible. Needless to say, when they all crash into each other, the worlds barely survive.
- In the Erebus Sequence, it takes until the end of the second book (of three) to be clear on exactly who the main villain is. The King and the Majordomo each seem dismissive of the other's belief that they're the one in charge, and apparent new primary threats (the reactionary Fonteins, the increasingly tyrannical Domina, etc.) turn out to be manipulated by the then-thought-dead Majordomo.
Live Action TV
- Angel: Darla wants revenge/reunion with Angel. Her actions prompt Sajhan to pull Holtz through time to kill Angel and Darla both. Holtz betrays Sajhan, who then seeks aid from longtime foes Wolfram & Hart, who play off both Sajhan and Holtz. Sajhan discovers this and banishes Holtz to another reality, then duels Angel. In the aftermath of that battle, Holtz returns with a new means of attacking Angel, while Wolfram & Hart lick their wounds. Who was the Big Bad? Not even Joss Whedon could tell you.
- The writers, same as every season.
- A later Big Bad takes credit for having set all of it in motion millennia ago as part of their plan to (re)enter and take over the mortal plane. The veracity of the claim is never tested but there's no evidence to dispute it either and several of the events involved would definitly make more sense with some otherworldly party pulling strings behind the scenes.
- Burn Notice season three started with a Big Good cop as the potential antagonist, then moved on to an Affably Evil fixer, followed by a Psycho for Hire, and culminating with a Terrorist Without a Cause. Apparently feeling that was too easy, the writers in season four go with The Mole, a Corrupt Corporate Executive, a stray Smug Snake, a returning Evil Counterpart, ANOTHER returning Evil Counterpart, all before the reveal of the actual Big Bad: The Mole from the beginning!
- Dai Shi is the initial and eventual Big Bad of Power Rangers Jungle Fury, though the title shuffles frequently. Carnisoar, Jellica and Grizzaka all take their turns on the throne, and it initially looks like the Phantom Beasts are going to take over before they betray Jellica and Dai Shi takes back his title.
- The Metal Gear games, especially the Mind Screw of Metal Gear Solid 2, and the non-canonical Ghost Babel, where the terrorist general, his mercenary Dragon/manipulator, and the U.S. government all mock the others as fools who are just being played by whoever is doing the mocking at the moment.
- Untangling who stands behind whom, with many false leads, is the entire point of Deus Ex.
- Super Smash Bros. Brawl, in the Subspace campaign, has... numerous Big Bads. This stems partly from the nature of the game - as a lumping together of the respective Nintendo mythologies, all the key villains come with their respective heroes.
- To elaborate, it at first seems that the Subspace Army is led by the Ancient Minister with Bowser and Wario working with them to take out the other fighters and collect them in their trophy forms. King Dedede is also collecting trophied fighters, but he's competing with the other villains and it turns out he's Good All Along as he was collecting the fighters so that he could give them timed badges that would revive them in case all the fighters were wiped out. Then it turns out that the real leader of the Subspace Army is Ganondorf and Ancient Minister was Forced into Evil in order to protect the R.O.B.s. THEN it turns out Ganondorf and the other fighters working with the Subspace Army were working under the Master Hand, who was in turn being controlled by the true Big Bad, Tabuu, the lord of Subspace.
- Myst has this in spades. The game begins when you meet two imprisoned brothers, each of whom tries to convince you that his brother is the one behind the disappearance of their father. As you complete the various stages to slowly free the brothers, you encounter clues to help you finally decide which of the two is the actual Big Bad. Turns out, they BOTH are.
- Final Fantasy VII introduces Shinra as the Megacorp oppressing the world. The it turns out Sephiroth is Cloud's Arch-Nemesis and the real threat. But it turns out the Shinra scientist Hojo created Sephiroth by experimenting on Jenova, but Sephiroth is still the bigger threat than either of them. And the party continues to come into conflict with Shinra throughout the game as they search for Sephiroth.
- Final Fantasy VIII has the Galbadians and President Deling as the Disc 1 villains, only to kill him off and reveal Sorceress Edea as the real villain at the end of the disc. Then Disc 2 ends with Edea's defeat and Disc 3 reveals she was under Demonic Possession by the real villain Ultimecia.
- Final Fantasy IX. The Big Bad is Queen Brahne. Wait, now it's Kuja! And now it's Garland! Now it's Kuja again! But in the end, it's Necron!
- The lattermost is more just the Final Boss - s/he/it has no involvement in the plot until then and isn't actually orchestrating anything (Necron is implicitly a personification of death/the reaper... probably).
- Seiken Densetsu 3 has three possible Big Bads, each with their own dragons and Mooks. About halfway the game, one of them will eliminate the other two (which one depends on your choice of main character), but until that time the whole game is a tangle of their conflicting plots.
- Assassin's Creed: The Templars/Abstergo are the oldest enemies of the Assassins and seem a lock for the position of Big Bads. But that's before you learn the Abusive Precursors who made the Pieces of Eden. Even then, it's a toss-up between Minerva and Juno until the end of III, which pretty clearly cements the latter.
- Batman: Arkham City has Hugo Strange and The Joker competing for the position of Big Bad, with Ra's al-Ghul proving to be Strange's hidden benefactor.
- Persona 4 is filled with this. First it seems that Kubo is the killer but he only killed your teacher and wanted attention. The murder attempts continue and you eventually find out that the one doing the deeds was Namatame but then it turns out that he thought he was doing good and something made him snap. The person who made him snap was Adachi who did the first two killings while Namatame did the rest, plus he threw Kubo in the TV world. AND THEN he gets possessed by Ameno-Sagiri, a creature that had been causing the fog and was using Adachi to raise paranoia and chaos among the town to begin to create a world full of shadows. AND FINALLY Izanami, one of the two gods in Japanese myth that birthed humanity, gave personas to you, Namatame, and Adachi to do what they did for her goals and is the master of Ameno-Sagiri. And I'm out of breath...
- Persona 3 is similar. At first the Full Moon Shadows serve as the collective Big Bad of the game, being the source of the Dark Hour. Then you meet Strega, a fellow group of Persona users who want to stop you from getting rid of the Dark Hour, but they aren't affiliated with the Shadows at all, they just want to keep using their powers for petty reasons (which mostly involve killing people). Their leader Takaya eventually manages to inflict a Plotline Death on one of your party members and is the closest thing the game has to a human villain. Then you kill all the Full Moon Shadows and Shuji Ikutsuki, your Mission Control, reveals himself as Evil All Along and that he was just using the party to bring about The End of the World as We Know It. This character becomes the clear new Big Bad... for all of one cutscene, after which they're quickly killed off and the game has No Antagonist for a while. Then we meet Ryoji, who turns out to be the avatar of Nyx, a godlike being that will bring about the end of the world. Takaya becomes The Dragon to this new Big Bad, and said new Big Bad is the Final Boss. However, the Playable Epilogue added in the Updated Re-release reveals that Nyx wasn't really evil and the true Big Bad, Erebus, was just using her to destroy the world. Though Erebus is more of an animalistic force born from humanity's collective despair than an actual sentient being, complicating things further.
- The third game in The Second Reality Project series is slated to have this, according to this old thread at SMW Central. The first world takes its time to set up the game's premise. Bowser, the Big Bad of the first game, returns to the Second Reality with the intention to take back the Power Supply Switch from the Catgoom Kingdom. Then it was discovered that Zycloboo, the second game's Big Bad, has been revived, and he too wants the Power Supply Switch. With both villains vying for the switch, Mario and his friends have no choice but to go on a quest to destroy it.
- Life Is Strange initially seem to set up either Nathan Prescott or Frank Bowers as the main candidates for Racheal Ambers disappearance and subsequent death. However Frank turns out to be a giant Red Herring (Rachael was actually in a relationship with him) and Nathan turns out to be The Dragon to the true villain of the game Mark Jeffison.
- Homestuck does this quite a lot. So, the Big Bad and Final Boss of the Game is the Black King. Except before they can fight him, he gets killed by Jack Noir, who's the REAL big bad that all the heroes and other villains are trying to stop. Except the whole thing was a set-up by Vriska Serket. Until it Jack stops following her plans. And then it turns out that they were both under the control of Doc Scratch, even though Jack is actually more dangerous than him, except he's not because everything he does is part of The Plan, and it eventually turns out that Scratch was behind everything. BUT WAIT! He was doing everything to summon his Master, Lord English, who's actions also provoked the Horrorterrors, pretty much the only party not being manipulated by someone. But then, Act 6 introduces even more villains while still keeping one or two of the old ones around, but all of them can be traced back to Lord English.