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- The Android Saga of Dragon Ball Z starts off with Androids 20 and 19 as the villains. Then it's revealed that they aren't the androids responsible for defeating the Z-Fighters in the future. Right after Androids 17 and 18 are introduced and kill Android 20/Dr. Gero. They look to be the true villains until Cell appears and absorbs them both, solidifying himself as the Big Bad of the saga.
- The Future Trunks saga of Dragon Ball Super initially presents Goku Black as the main villain. Later on though, we learn that Goku Black is actually working with Future Zamasu to exterminate the mortals, though their relationship is left ambiguous. Whis theorizes that Black is actually a servant created by Future Zamasu to act as The Dragon to him. However, it is eventually revealed that Goku Black is actually an alternate Zamasu, and he is the one who came up with their plan in the first place. Despite this, the two seem to have a pretty solid Big Bad Duumvirate between them and they later merge into a singular Big Bad, Fusion Zamasu.
- The Big Bad of Naruto has, at various points, been: Orochimaru (former Akatsuki member) -> Akatsuki itself (Itachi being its most visible player) -> Pain (with Tobi as true Big Bad) -> Tobi and Danzo -> Kabuto and Tobi -> Madara and Obito -> Obito (when he becomes the jinchuuriki of the Ten-Tails and Madara leaves on second plan) -> Madara (after defeat Obito) -> 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).
- Kill la Kill starts off with Student Council President Satsuki Kiryuin as the Big Bad. Halfway through, it's revealed that Satsuki actually been working to fight the real Big Bad, her mother, Ragyo Kiryuin, who is also The Dragon to the Primordial Life Fiber.
- 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.
- Yu-Gi-Oh! 5D's, the initial antagonists are Jack Atlas, The Rival, and Sector Security and their leader, Rex Godwin. Then in the second half of Season 1 the heroes find out Rex has been recruiting the heroes to fight the Dark Signers and his brother Roman, the real villains. Then Rex becomes a Dark Signer as well and becomes the Final Boss of the season. Next season the Three Emperors of Yliaster become the main antagonists, and it is revealed Roman and Rex were their puppets they manipulated. The Three Emperors in turn are working for the leader of Yliaster, Z-one. It is also revealed that the Big Bad of the 10th Anniversary film, Paradox, was another member of Yliaster.
- 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.
- The Ascendant Kingdoms Saga has, at various points, Pentreath Reese, Vigus Quintrel or rather, the demonic being controlling Quintrel and Thrane as architects of different plots trading off the role of main threat; Lord Vedran Pollard is The Heavy of the series and works with or for all three of the above at various points to advance his own ambitions, and Nagok has a similar relationship with Thrane alone. However, several characters speculate that Thrane may have been responsible for the magical cataclysm that set the Myth Arc in motion; if this is true, that probably cements him as the Big Bad of the Saga.
- Codex Alera combines this with Big Bad Ensemble, as some of them overlap: For the first book, it's the Atsurak (with the Aquitaines as the Greater Scope Villain), then it's Sarl in book two, Lord Kalare and Sarl in Books 3, Kalare and Senator Arnos (with Lady Aquitaine pulling his strings) in Books 4 and 5, it's the Vord Queen.
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!
- Game of Thrones: The multiple storylines that occur indepedently of each other, as well as the shifting morality and power structures of the various noble houses and other factions, results in there being several central villains at a time. Among the top contenders across the series are Tywin Lannister (the head of House Lannister and thus an enemy to the Starks and Baratheons), Littlefinger (actively instigated the War of the Five Kings), Roose and Ramsay Bolton (evil overlords of the North and enemies of the Greyjoys), the High Sparrow (religious fanatic who is taking over King's Landing), Mance Rayder (the leader of the Wildlings planning to attack the Night's Watch), and most unquestionably, the White Walkers, who are plotting to invade Westeros and Kill 'em All.
- 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.
- Kamen Rider Gaim goes through this as more of the story is unveiled and important details surface. When the Invase first appear, it looks like Takatora Kureshima (Kamen Rider Zangetsu) and his Yggdrasil Corporation are behind it. Then it turns out he's trying to save humanity, but everything is thrown into chaos by the reveal of a metaphorical and literal Apple of Discord: Takatora gets back-stabbed by his power-hungry inner circle and his younger brother Mitsuzane. Then the characters learn that the Invase have intelligent leaders called "Overlords", who possess the Golden Fruit everyone wants. Then Mitsuzane undergoes a full love-induced Face–Heel Turn, including allying with one of the Overlords who wants the Fruit for herself. In the end, The Rival Kaito Kumon (Kamen Rider Baron) is the "final boss" because his Social Darwinism clashes with The Hero Kouta's more benevolent attitude and they fight for ownership of the Fruit.
- The Call of Duty: Modern Warfare games go through several Big Bads. In the first game, Al-Asad, the leader of a revolution in a nameless Middle Eastern country looks to be the Big Bad at first. Halfway through, it's revealed that his revolution was being funded by Russian Ultranationalist leader, Imran Zakhaev. After Zakhaev is disposed, one of his Co-Dragons, Vladimir Makarov, appears to fill the Big Bad role in Modern Warfare 2. However, it's eventually revealed that Makarov was an Unwitting Pawn of General Shepherd. However, Modern Warfare 3 reveals the Makarov may have been using Shepherd as his pawn, and that he's the one who detonated the nuke that drove him mad. He also saved Zakhaev when he was shot, ultimately making him responsible for the events of the Modern Warfare series as a whole.
- 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).
- Final Fantasy XIV. The game starts off with a series of Garlean superior officers on the surface - Nael van Darnus in 1.0, who along with Bahamut caused the Calamity; Gaius van Baelsar in 2.0 who acts as the Empire's The Heavy as they invade Eorzea; Regula van Hydrus in 3.0 who replaces Gaius and even brings along Emperor Varis as the Greater Scope Villain for the Empire. The Ascians, with Lahabrea, Nabriales (pre-3.0), and Igeyorhm (during 3.0), working from the shadows form the majority of the overall conflict of the story. Then 3.0 reveals that King Thordan of Ishgard is driving most of the plot and is the true Big Bad of the 3.0 plotline, manipulating the Ascians while they think they're manipulating him. Meanwhile, each of the city-states have their own minor antagonists (who are usually underlings to one of the above), but Lord Lolorito of Ul'dah has been orchestrating a lot behind the scenes and may be a step ahead of them all if he gets Omega in possession like he's planning to.
- 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 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.
- 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 5: Each Arc Villain was being pressured into The Conspiracy by someone in a "Black Mask". Black Mask was in turn working for politician Masayoshi Shido. And the villains and the heroes were being manipulated by the real Big Bad, Yaldabaoth, God of Order.
- 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.
- Neverwinter Nights, the expansion Shadows of the Undrentide opens with a tribe of kobolds attacking your home and stealing several artifacts. As you pursue them you find evidence that they came into conflict with some bugbears and each made off with at least one artifact. The kobolds are employed by the dragon Tymofarrar, but he ordered the attack because he was in alliance with J'Nah, the leader of the bugbears. Then you find out J'Nah is collecting the artifacts for a unknown third party.
- Chrono Cross winds up doing one in its final act, due to its enormous Gambit Pileup finally getting resolved. For most of the game, the apparent Big Bad is Lynx - who turns out to be an avatar of the rogue supercomputer FATE. Defeating FATE, however, allows the Dragon Gods to return to their true form and busily get to work on destroying humanity. And it's only after you defeat the Dragon Gods that you learn the entire plot was orchestrated as a setup to create a weapon capable of defeating the real Big Bad, the Time Devourer.
- In Guild Wars Prophecies, the first campaign, the game begins with the Charr being set up as big bads and destroyers of the player characters' home kingdom. Then they travel through the Shiverpeak mountains with the Stone Summit Dwarves taking over their role as primary antagonists, especially when they kill Prince Rurik. When the PC's arrive in Kryta however, the undead and the Lich Lord pop up as a new bad until they find out the truth about and are betrayed by the White Mantle who then proceed to hunt them down for a good portion of the game. The player characters then go through a lot of trouble to Ascend and be able to see and fight their "gods" the Mursaat, when suddenly they're thrown back against the Stone Summit Dwarves and finally deal with their leader, then back to the Mursaat. Then out of the blue it turns out that one of their closest allies of the last half of the game was in fact the Lich Lord in disguise and he uses their actions to take control of the Titans, another race of superpowered baddies, and they end up facing him as the final big bad.
- Halo 2 starts off with the three Covenant High Prophets in a Big Bad Triumvirate. However, after the Prophet of Regret gets killed by Master Chief and the Prophet of Mercy gets devoured by the Flood, leaving the Prophet of Truth as the sole Big Bad. He soon forms a Big Bad Ensemble with the Gravemind, though in Halo 3 the Gravemind and the Flood briefly team up with our heroes to stop Truth from activating the Halo Rings. After this gets accomplished, the Gravemind takes over the sole Big Bad.
- 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.
- The initial Big Bad of Madness Combat is the Sheriff, though after Hank kills him, his Dragon Jesus briefly takes the role. Then Tricky comes in and kills him, stealing the role from him. It's eventually revealed though, that the overall Big Bad was the Auditor, as he was manipulating everything through the Improbability Drive.
- One episode of Gargoyles featured six villains, each revealing one after the other that the previous villain wasn't actually that episode's Big Bad.
- Season 20 of South Park at first presents a Big Bad Ensemble between SkankHunt42 / Gerald and Mr. Garrison, who are soon joined by the Memberberries. A few episodes later, they are also joined by Lennart Bedrager, head of TrollTrace.com, who eventually takes Gerald out of commission. Mr. Garrison, meanwhile, ends up becoming a pawn of the Memberberries, who are also revealed to be led by the Don Memberberry. However, the Memberberries become Out of Focus when Lennart and TrollTrace take center stage, leaving Lennart as the Final Boss of the season.