History Main / HijackedByGanon

* ''Fanfic/JWITCHSeason1'': Just like in canon, Shendu's resurrection by Daolon Wong sees him easily supplant the wizard and every other villain in the story as [[EvilerThanThou the worst one around]] -- he overpowers [[spoiler: and kills]] Cedric, [[DestinationDefenestration tosses Wong and Miranda out windows]] and ''far'' away from the castle, and blasts Phobos through his own throne.

* In ''Machinima/ArbyNTheChief'', Chaos Theosis, the main antagonists of Season 6, were actually working for Trent Donnovich, who was the main antagonist of Season 5.]

** ''ComicBook/TheChildrensCrusade'' retroactively paints Doctor Doom as the one behind the Scarlet Witch going insane, leading to ''ComicBook/AvengersDisassembled'' and ''ComicBook/HouseOfM''.

* ''Franchise/WonderWoman'': Taken UpToEleven in ''ComicBook/AmazonsAttack''. A brainwashed Queen Hippolyta has led the Amazons of Themyscira to wage war on the United States! BUT WAIT! It turns out that Queen Hippolyta's attack was actually all a SecretTestOfCharacter by the goddess Athena! BUT WAIT! It turns out it was all a convoluted plot masterminded by Granny Goodness of the ComicBook/NewGods while ''disguised'' as Athena and keeping the other Greek gods imprisoned! BUT WAIT! The entire miniseries was actually a tie-in to ''ComicBook/CountdownToFinalCrisis'', where Granny Goodness is training hundreds of women to be female furies in connection to the Death of the New Gods! BUT WAIT! [[FourLinesAllWaiting The Death Of The New Gods/Jimmy Olsen's superpowers plotline]] from ''Countdown'' was actually all part of Darkseid's evil plan involving the Anti-Life equation, and Granny Goodness was just working for him! [[KudzuPlot WHAT.]]

** The fic takes this UpToEleven with its initial premise, with Demise (having very, ''very'' slowly managed to extract himself from the seal within the Master Sword) finally getting fed-up with the incompetence of the incarnations of his hatred and hijacking ''all of them''. As the Links find out, this also gives him ''all'' of their powers, on top of the fact that he's a PhysicalGod (they spend most of the [[CurbstompBattle 'fight']] running for their lives and screaming, and they require a literal DeusExMachina from the Goddesses to survive). Doing this also happens to rip open some rather large holes in reality, which expand to consume everything they touch, destroying reality - [[OmnicidalManiac which suits Demise just fine]]. The fact that the Goddesses hijack them as a PortalNetwork for the collected Links, not so much.

** Before his fate was {{retcon}}ned by ''WesternAnimation/StarWarsTheCloneWars'' and ''WesternAnimation/StarWarsRebels'', Darth Maul came BackFromTheDead several times before being finally reduced to a [[BrainInAJar brain & spine in a bacta tank]] controlling a HardLight hologram. Luke Skywalker then finishes him off once and for all by shutting down his life support.

A subtrope of TheManBehindTheMan, where an old villain is behind a new one.

A SubTrope of ObviousVillainSecretVillain. Might be the result of the new villains managing to ResurrectTheVillain or the old villain being a ReturningBigBad. The inversion of MakeWayForTheNewVillains. Contrast NotMeThisTime. See also DiabolusExNihilo and TheManInFrontOfTheMan.

* Mocked in ''[[WebAnimation/SoThisIsBasically So This Is Basically Legend Of Zelda]]'' describes Ganondorf as having the evil power of plagiarism and shows him dangling the deed to the Twilight Realm above Zant's head.

[[folder:Western Animation]]
* More than one ''WesternAnimation/AdventureTime'' plot has turned out to have the Ice King behind it, occasionally nonsensically. This was likely parodied in the season 2 finale, where all he did for the first part was hang around annoying everyone and trying to be involved in the story, even though there was a bigger villain around.
* The ''WesternAnimation/AdventureTimeDistantLands'' episode "Together Again" introduces a new antagonist, New Death, who wants to destroy all the realms of the afterlife and stop the cycle of reincarnation. Only at the end does it turn out he was being manipulated by the Lich the whole time, who continues his pursuit of [[OmnicidalManiac killing everyone in existence]], even after death. It's a fitting sendoff because the episode is the GrandFinale of the entire series and Finn and Jake are facing off against the effective BigBad of the story once again, even at the very end.
* The season 3 finale of ''WesternAnimation/{{Archer}}'', "Space Race", has Archer and the ISIS crew board a space station to stop a mutiny, only to get caught in the station commander's plan to colonize Mars. Once he commits suicide, it seems for the moment they only have to worry about getting back planetside- until Barry, Archer's cyborg rival who is hellbent on killing him ([[ItMakesSenseInContext long story]]), just happens to show up (having known he'd be there thanks to Kreiger).
* The Ba Sing Se arc of ''WesternAnimation/AvatarTheLastAirbender'' played up [[ChessMaster Long Feng]] as the storyline's BigBad. But then [[MagnificentBastard Princess Azula]] came along and took center stage. Long Feng, on his part, actually saw this trope coming and attempted to betray her, but unfortunately for him, [[OutGambitted Azula managed to turn his own soldiers against him.]]
* ''WesternAnimation/TheLegendOfKorra'': It's revealed in "The Stakeout" that Zaheer and his gang are part of a group called the Red Lotus, which [[EvilUncle Unalaq]] (TheHeavy in Book 2) was initially part of.
* Season 3 of ''WesternAnimation/Ben10'' introduced in one episode a werewolf-like alien who was seemingly killed at the end of his episode, but was revealed to have built a machine as a SequelHook. A mummy-like alien is then introduced in a later episode. Both come back and are revealed to work for a new villain named Dr. Vicktor in the first part of the season finale...and then it turns out Dr. Vicktor himself was TheDragon to Ghostfreak/Zs'kayr, a villain who had been introduced in a previous season 2 episode.
* Both seasons of ''WesternAnimation/Ben10UltimateAlien'' used this trope:
** Season 1 featured MagnificentBastard Aggregor as the main antagonist, whose scheme remained unstoppable for most of the season...then, when it was about to succeed, [[TheAtoner Kevin]] sacrificed his sanity by using [[WithGreatPowerComesGreatInsanity the part of his power that would cause him to go crazy again]] to stop him. After he is defeated, Kevin, now back to being a psycho, serves as the main villain for the remaining episodes of the season.
** Season 2 is even more complex; it starts with a BigBadEnsemble involving a war between the Forever Knights and a new, mysterious sect that turns out to be manipulated by Ben's ArchEnemy Vilgax. Then an EldritchAbomination Vilgax had been impersonating shows up and takes Vilgax as his Dragon, apparently becoming the new BigBad...until Vilgax [[TheStarscream betrays]] him, absorbs him and becomes the final villain of the season.
** ''WesternAnimation/Ben10Omniverse'' has an InUniverse example. In the first 10-episode arc, [[EgomaniacHunter Khyber the Huntsman]] is the BigBad. In the 2-part finale however, it's eventually revealed he actually is working for [[TheManBehindTheMan Dr. Psychobos]], an EvilGenius Cerebrocrustacean who invented Khyber's main weapon, the Nemetrix with the aid of [[GreaterScopeVillain Malware]], a PredecessorVillain who was introduced in this series, but whose first appearance chronologically happened between [[WesternAnimation/{{Ben 10}} the original series]] and ''[[WesternAnimation/Ben10AlienForce Alien Force]]'', and who had only been seen in flashback at this point.
* In ''WesternAnimation/{{Gargoyles}}'', for a large chunk midway through the series a group of [[PowerTrio three god-like beings]] [[TheFairFolk called the Weird Sisters]] pop up from time to time, manipulating the main cast for their own ends. It turns out in the epic three-part episode "Avalon" that they were answering to [[EvilSorcerer the Archmage]], a previous villain who was believed to be dead, and all their plotting had been to help him conquer the titular island (or at least that's what they told ''him'' they were doing...) It would probably be better to say they were [[DragonWithAnAgenda Dragons With An Agenda]]. The trope still stands, however.
* ''WesternAnimation/{{Hurricanes}}'': In "Escape to Freedom", the Hurricanes were captured by a soccer-obsessed General of a BananaRepublic and forced to play against his soccer team. It was revealed to the viewers but not to the Hurricanes (albeit it's implied the team's owner suspects) [[BigBad Stavros Garkos]] made an agreement to keep them from showing up for an upcoming game so Garkos' own team, the [[OpposingSportsTeam Garkos Gorgons]], would win by default.
* Season 3 of ''WesternAnimation/JackieChanAdventures'' has the Season's BigBad, Daolon Wong, resurrecting Shendu in order to obtain the wayward [[PlayingWithFire Dragon Talisman]] power. [[EvilIsNotAToy The results are obvious]].
* In ''WesternAnimation/JusticeLeague''
** It's revealed that Lex Luthor was being manipulated by Brainiac to build him a new body. Luthor had been infected by a copy of Brainiac's programming after Brainiac had exploded the last time he and Luthor had met.
** More to the point, Luthor and Brainiac take over the BigBad post from [[GovernmentConspiracy Cadmus]] by showing Luthor had manipulated Cadmus, gaining access to their technology so he could build a new AMAZO [[BrainUploading and upload his mind]] (or, rather, Brainiac's mind) into it. The writing staff [[WordOfGod admitted on the DVD commentary]] that they had no idea how to make the plot of season 2 untangle on its own due to the GreyAndGrayMorality situation that had arisen, so they went with an "old reliable" and let a BlackAndWhiteMorality villain take over [[InvokedTrope so they could have a proper fight finale]].
** In the subsequent story arc, this happens ''twice''. Gorilla Grodd's leadership of the Legion of Doom is usurped by Luthor, then Lex's plan to reassemble Brainiac is throttled when he accidentally brings back Darkseid instead.
* In ''WesternAnimation/LegionOfSuperHeroes'', Imperiex, season 2's BigBad, teams up with Brainiac 5 (Who had been taken over by the programming of Brainiac 1.0). Just as Imperiex broadcasts their alliance to the Legion, Brainiac 5 [[ImpaledWithExtremePrejudice impales]] and disintegrates Imperiex, then takes control of Imperiex's forces himself.
* ''WesternAnimation/MyLittlePonyFriendshipIsMagic'':
** {{Double Subver|sion}}ted. When vines from the Everfree Forest started invading Ponyville and the princesses went missing in the episode "[[Recap/MyLittlePonyFriendshipIsMagicS4E1PrincessTwilightSparklePart1 Princess Twilight Sparkle]]", everyone assumed it was a new threat or villain causing all this. In [[Recap/MyLittlePonyFriendshipIsMagicS4E2PrincessTwilightSparklePart2 Part Two]] it seems to be because of Luna becoming Nightmare Moon again, when it's revealed that it was all a flashback. Then it gets double subverted at the end. It turned out that it was caused by seeds that the recently reformed villain [[MadGod Discord]] planted right before his defeat by Celestia and Luna over a millennium before. [[UnintentionalBackupPlan The Tree of Harmony's power managed to keep them from growing for that long]].
** A literal variation happens in [[Recap/MyLittlePonyFriendshipIsMagicS9E24TheEndingOfTheEndPart1 the series finale]]. Throughout the ninth season, it looked like it was buiding towards [[AncientEvil Grogar]] being the FinalBoss of the series, with him bringing together Equestria's remaining unreformed villains into a LegionOfDoom and having them [[DemotedToDragon under his hoof]]. It turns out, however, that it was actually Discord in disguise, [[WellIntentionedExtremist though he did so with good intentions]], planning to use the villains [[EngineeredHeroics to give Twilight some easy victories]] to boost her confidence as the new ruler of Equestria. Unfortunately, the villains managed to outsmart him, double-crossed him, and used the Bewitching Bell [[BroughtDownToNormal remove his magic]] so he couldn't keep them in line, leaving them to be the true final threat of the series.
* ''WesternAnimation/RickAndMorty'': "Vindicators 3: The Return of World Ender" has Rick and Morty joining the Vindicators, who are trying to prevent [[ExactlyWhatItSaysOnTheTin the return of World Ender]]. When they find World Ender on his home planet, it turns out he's already been killed; all of them immediately assume [[AlwaysABiggerFish an even more powerful villain is responsible]]. That more powerful villain turns out to be [[VillainProtagonist Rick himself]], who killed World Ender while blackout drunk, and also set up a number of ''Film/{{Saw}}''-style traps which end up killing all but one of the Vindicators.
* ''WesternAnimation/RockyAndBullwinkle'': It doesn't matter who or what's causing trouble in Frostbite Falls or anywhere else in the world. In the end, either Boris is ''always'' going to be the one causing all the mayhem, or if he ''isn't'' the antagonist of the episode, they're going to bring him in to help them out. The exception is "The Ruby Yacht", where he does not get involved at all.
* The story of ''WesternAnimation/StevenUniverse'' relies heavily on the Matriarchal Diamonds who run the entirety of Gem society. Blue and Yellow Diamond serve as major antagonists for the vast majority of the series, however the series teases that there have been a total of four diamonds. With the fate of Pink Diamond known, and both Yellow and Blue Diamond finally pacified, the story immediately shifts to White Diamond. At this point, White Diamond becomes the de-facto focus of the story, and the fear that Yellow and Blue show when speaking of her actions makes it obvious that White is the one in absolute charge of Homeworld.
* In the second season of ''WesternAnimation/{{WITCH}}'', the first season's BigBad, Phobos, escapes in one episode and takes over a team of recurring vilains, the Knights of Vengeance, from Nerissa. Justified in that they were [[TheRemnant Remnants]] of his army and still loyal to him and that Nerissa didn't need them anymore anyway. He was quickly defeated by Eylon and Nerissa reclaimed her position of BigBad by tricking Eylon into giving up her powers. After Nerissa later acquired the powers of the Heart of Dumbala, the girls grew desperate and decided to [[EnemyMine ally themselves with Phobos]] as only a member of the Meridian royal family was capable of forcibly taking the Heart of Meridian. This, of course, ended with him stealing Nerissa's powers, reclaiming his army and throne while setting his sights on [[MultiversalConqueror multiversal conquest]]. At least until Cedric pulled a [[TheStarscream Starscream]] and stole ''his'' powers.
* In the ''WesternAnimation/CaptainNTheGameMaster'' episode "Quest for the Potion of Power," Mother Brain uses the titular potion to revive Ganon so she can control him.[[note]]Only the original NES games existed at the time of the cartoon, so Mother Brain was essentially hijacking the plot of ''VideoGame/ZeldaIITheAdventureOfLink''.[[/note]] Three guesses how that went.
[[/folder]]

[[folder:Video Games]]
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%%Please don't list aversions (i.e. games where a series-wide villain either doesn't appear at all or does appear and is stated to be the primary villain from the start)
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* ''VideoGame/AceCombat'':
** Played as an InternalReveal in ''VideoGame/AceCombat5TheUnsungWar'': the masterminds behind the war between Osea and Yuktobania turn out to be the same rich Belkan nationalists who sponsored the Belkan War fifteen years earlier. However, this was the first time that the Belkan War was even mentioned in the ''AC'' canon at that point, and the prequel expanding on it, ''VideoGame/AceCombatZeroTheBelkanWar'', wouldn't come out for another two years.
** ''VideoGame/AceCombat6FiresOfLiberation'': Downplayed here, while the main story never reveals it, the designer of the Aigaion Heavy Command Cruiser was a Belkan pilot who defected to Estovakia after the Belkan War, Lorenz Riedel a.k.a. Gault 7. You have to find this out by reading the supplementary info. The Aigaion was absolutely crucial to the Estovakian invasion of Emmeria; even if Riedel wasn't actually directing the war, it wouldn't have happened without his involvement.
** ''VideoGame/AceCombat7SkiesUnknown'': Where did Erusea get their super-advanced aerial drone fleet? From Belkans! And the head scientist of the Erusean Air & Space Administration behind the drones is the brains behind the technology, following a spiteful legacy spread by Belkan patriots to cause as much chaos and destruction across the world as they can in revenge for losing the Belkan War.
* In the ''VideoGame/BatmanArkhamSeries'', ComicBook/TheJoker is always the real BigBad.
** In ''[[VideoGame/BatmanArkhamAsylum Asylum]]'', it's fairly straightforward; Joker engineered the prison break at the titular Asylum.
** In ''[[VideoGame/BatmanArkhamCity City]]'', while trailers did feature the ensemble, it seemed that Hugo Strange and TYGER would be much more the overarching threat, Strange ended up being a pawn of Ra's, who you already beat earlier in-game, and both of them died in the same cutscene. Their plan to launch "Protocol 10" is seldom referenced in the entire game, while Joker's plot to force Batman to find a cure for his TITAN poisoning gets the most screen time, up to the final confrontation of the game.
** In ''[[VideoGame/BatmanArkhamOrigins Origins]]'', trailers hyped up Black Mask, a relatively unknown villain to non-comic fans, as the BigBad who hired eight assassins to kill Batman. It was really Joker pretending to be Black Mask the whole time. Joker is arrested and sent to Blackgate Prison at some point while some of his assassins and other villains are still roaming free, but he causes a prison riot and is the final opponent of the main storyline.
** Unsurprisingly, ''[[VideoGame/BatmanArkhamKnight Knight]]'' follows suit -- Scarecrow and the Arkham Knight are the BigBadDuumvirate, but the Joker's the GreaterScopeVillain. Even though Joker is dead -- and the game starts with the heroes cremating him just to make sure -- he still massively influences the plot; his death leads to the other rogues uniting against Batman, people are still infected with his tainted blood, and he created the Arkham Knight - aka Jason Todd. Oh, and he keeps appearing to Batman as a hallucination because Bats is one of the tainted. The end conflict is as much Batman fighting off Joker's influence as it is him resisting Scarecrow's fear toxin.
** In fact, the only story campaign in the entire series that doesn't feature the Joker's influence ''at all'' is ''[[VideoGame/BatmanArkhamOrigins Origins]]''' "Cold, Cold Heart" DLC.
* ''VideoGame/BlasterMasterZeroIII'': As the game continues, Jason is led to believe that the Mutant Core from the first game has made yet another comeback. There was a comeback, but it was not the Mutant Core, which stays gone. The actual comeback was done by Planade-G, whose core survived its defeat in the second game and went on to kidnap Eve, subjugating her to gain control of the mutant army.
* ''Franchise/BlazBlue'' has a pretty active BigBadEnsemble, but ultimately Yuuki Terumi is the overall BigBad with the largest influence on the plot. He takes center stage in [[VideoGame/BlazBlueContinuumShift the second game]] along with his partner-in-crime [[MadScientist Relius Clover]], but they're both ultimately pushed aside in [[VideoGame/BlazBlueChronophantasma the third]] for Hades: Izanami, [[PhysicalGod the goddess of death]] in the third game and Terumi is rather unceremoniously killed off...[[JokerImmunity except he wasn't]]. Come [[VideoGame/BlazBlueCentralFiction the fourth game]], both Izanami and their EvilGenius Nine take center stage as the primary threats, with Relius hanging in the background to observe the events and Terumi hanging on by a thread to survive. After Izanami and Nine are defeated, Relius decides to pull a VillainExitStageLeft, leaving Terumi, or rather his true form as Susano'o, as the sole BigBad and the FinalBoss of the series. It's even revealed that Terumi was indirectly responsible for the other villain's plots as well.
* ''VideoGame/BoxxyQuestTheGatheringStorm'' has ''three'' examples:
** The game is purportedly a standalone story, unrelated to its prequel except for a few small nods here and there. Then comes Chapter 7, a flashback WhamEpisode dealing with the origins of the first game's BigBad, Boxxyfan. And then it turns out that the Pale Wraith is his VirtualGhost, and the sequel's entire plot was set up by him as a gambit to regain his original avatar. He succeeds in the first ending's [[TheStinger Stinger]], and goes on to fully reclaim his Big Bad status during the True Ending bonus episode. (Let's note that while this is a twist, it's not entirely out of left field -- the game comes packaged with a summary of the prequel's plot, which implies that it's going to be relevant in some way.)
** Legion is the primary villain of the backstory and Chapter 7, which takes place during said backstory, but seems to disappear from the plot afterwards, his only role being to give Anonymous inner conflict. Then Boxxyfan accidentally revives him and he promptly becomes the final BigBad, usurping the role from Boxxyfan.
** Originally Rcoastee, the ''other'' BigBad of the first game, was going to appear in the bonus Easy Mode quest and turn out to be behind the dark happenings, but the quest got cut. However, he ''does'' appear in the Alwaysland 2 DLC BonusDungeon as a {{Superboss}} and attempts to delete Catie and her friends.
* The ''VideoGame/BubbleBobble'' {{spinoff}} ''Bust-A-Move'', AKA ''Puzzle Bobble'': In the VS CPU modes of installments 2 through 4, an enemy named Drunk (the green hooded beer-drinking enemy from Bubble Bobble) has been inside, respectively, a giant robot {{Mecha}} named Bubblen (one letter shy of Bub's ''long'' bubble dragon name), a giant fake bubble dragon named Debblun, and a spaceship face named Madam Luna.
* The UsefulNotes/ArcadeGame ''VideoGame/CaptainAmericaAndTheAvengers'' openly presents Red Skull as the BigBad. The NES version [[ReformulatedGame isn't exactly based on it]], but it's not hard to guess who the "Mystery Big Boss" is.
* Dracula ''loves'' to do this in the ''Franchise/{{Castlevania}}'' games. He's the final boss almost every time, whether he's been visibly in play from the start or not.
** ''[[VideoGame/CastlevaniaSymphonyOftheNight Symphony of the Night]]'' is a classic example; [[RogueProtagonist Richter Belmont]] ''seems'' to be the villain, until you find out he was possessed by Shaft from ''[[VideoGame/CastlevaniaRondoOfBlood Rondo of Blood]]'', who orchestrated this as another raising-Dracula ritual. You only get to know this if you explore the castle thoroughly, though, and equip the Holy Glasses you get by doing so. Then you can see what's possessing Richter, and kill it. If you don't free Richter from his curse, you get the BadEnding by killing him. And you miss the Inverted Castle, which makes up another half of the game to get to Dracula.
** Subverted in ''[[VideoGame/CastlevaniaChroniclesOfSorrow Aria of Sorrow]]'' with a TomatoInTheMirror -- you can't expect to ''fight'' Dracula if you're ''playing'' him, right?
** Its sequel ''Dawn of Sorrow'' deliberately allows you to play this trope straight: fail to equip a certain item before entering the endgame, and Dracula successfully takes over control of your player character, kills off the former main villain, and becomes the BigBad of [[ArrangeMode Julius Mode]].
** ''[[VideoGame/CastlevaniaPortraitOfRuin Portrait of Ruin]]'' has another vampire, Brauner, take control of the castle. After you beat him, Death kills him and Dracula is revived once again.
** And in ''[[VideoGame/CastlevaniaHarmonyOfDissonance Harmony of Dissonance]]'', which had, as a "novelty" that Dracula ''didn't'' appear...He kind of just appears anyway. [[CameBackWrong As a wraith]], but still.
** ''VideoGame/{{Castlevania 64}}'': You know that kid Malus? The one who claims he was kidnapped by Dracula's followers along with the other children? He ''is'' Dracula. That vampire you fought earlier in the game was a fake.
** In both ''[[VideoGame/CastlevaniaCurseOfDarkness Curse of Darkness]]'' and ''[[VideoGame/CastlevaniaOrderOfEcclesia Order of Ecclesia]]'', Dracula yet again comes out of nowhere at endgame. This time, it's thanks to GrandTheftMe, although the former is a {{plan}}[=/=]ThanatosGambit carried out by Death, while the latter is an unintended aftereffect of Albus absorbing one of the pieces of Dominus (i.e. Dracula's power), although [[TreacherousAdvisor Barlowe]] has a hand to play in Drac's revival as well.
** More or less, the ''Castlevania'' series ''runs'' on this trope. If Dracula is not directly mentioned, heard from, or seen, or it is not specifically stated that his followers (most likely [[DragonAscendant Death]], although others have taken up the helm before) are attempting to resurrect him, then there's at least a 90% chance Dracula is ''still'' behind it all. In fact, as ''[[VideoGame/CastlevaniaLamentOfInnocence Lament of Innocence]]'' can attest to, Dracula was hijacking the plot ''[[BatmanGambit before he even]] [[BigBadFriend canonically became Dracula]]''.
** The entire plot of ''VideoGame/CastlevaniaJudgment'' is preventing Dracula from being Hijacked by Galamoth (of ''VideoGame/KidDracula'' and ''[=SotN=]'' fame).
** ''[[VideoGame/CastlevaniaLordsOfShadow Lords of Shadow]]'': Gabriel Belmont was the man who would become Dracula the entire time. Congratulations player! You just hijacked the BigBad title from the Lords of Shadow and {{Satan}}.
* After switching primary villains a dizzying number of times in the first place, the final boss of ''VideoGame/ChronoCross'' ends up being Lavos (or, at least, a version of Lavos), just as in [[VideoGame/ChronoTrigger its predecessor]].
* In ''VideoGame/CityOfHeroes'':
** Nemesis orchestrated the [[AlienInvasion Rikti invasion]] and possibly the [[NoSwastikas Council overthrow of the 5th Column]]. However, the events in [[AncientRome Cimerora]] were started by a different group of villains: the Nictus, including Requiem and the 5th Column.
** The [[AncientRome Cimerora]] zone was only introduced after the appearance of [[TimePolice Ouroboros]] whose chief, Mender Silos, has a SignificantAnagram.
** True veterans of the game know it's only a matter of the time until the writers make Nemesis responsible for all of the Nictus and Kheldian plots entirely as well. The game [[LampshadeHanging pokes fun at this]]. "It's all a Nemesis plot", "Not everything is a Nemesis plot", and "If it wasn't a Nemesis plot already, you can use the Mission Architect to make it one" are all tips on loading screens.
** The Nemesis version is subverted in the Issue 19 med-porter arc: Your contact realizes the two enemy groups wouldn't work together on their own, and both groups have canonical ties to Nemesis, so he'd be the natural suspect even if he weren't behind everything else. However, it turns out to be Malta pulling the strings.
* In ''Videogame/CommandAndConquerRedAlert3'', the newly introduced faction, the Empire of the Rising Sun, is treated as an emerging threat, enough to catch both the Soviets and the Allies by surprise. It's so bad that in the Allied campaign (and the Imperial one, for that matter), the Allies and Soviets sign an uneasy alliance in order to fight off the Japanese army. However, in both the Soviet and Allied campaigns, the Empire is swiftly pacified in the seventh mission in a nine mission campaign. The remaining two missions involve the Allies and Soviets fighting each other as they did before, both in this game and previous entries.
* ''VideoGame/CommanderKeen'' does this with both major trilogies -- it turns out the "Grand Intellect" manipulating the Vorticons is actually Mortimer [=McMire=], Billy Blaze's rival from school. Then it turns out the ruler of the Shikadi, the "Gannalech", is just [=McMire=] again (the Shikadi heard "Grand Intellect" but couldn't pronounce it). Also, his babysitter Molly from ''Aliens Ate My Babysitter'' turns out to be Mortimer's sister.
* In ''Franchise/{{Danganronpa}}'', Monokuma/Junko Enoshima will turn out to be the real mastermind even in games which appear to have a different antagonist, which is impressive considering she died in the first game.
** In ''VisualNovel/Danganronpa2GoodbyeDespair'', the mastermind is her VirtualGhost who hijacked the Neo World Program.
** In ''LightNovel/DanganronpaZero'', Junko, who masterminded the Hope's Peak conspiracy, temporarily wiped her own memory to become the protagonist Ryoko Otonashi.
** In ''VideoGame/DanganronpaAnotherEpisodeUltraDespairGirls'', Junko AIs were controlling Shirokuma and Kurokuma, meaning she was manipulating both sides of the entire conflict and is responsible for the Warriors Of Hope becoming soldiers of [[ApocalypseCult Ultimate Despair]]. These are then recovered by [[GreaterScopeVillain Izuru Kamukura]], leading to the events of ''2''.
** Subverted in ''Anime/Danganronpa3'''s Future Arc, where Junko has nothing to do with the Final Killing Game. Played straight in the Despair Arc where she literally hijacks the plot midway and it is shown how she plunged the world into despair.
** [[PlayingWithATrope Played with]] in ''VisualNovel/DanganronpaV3KillingHarmony'', in which the mastermind, upon being cornered, cosplays as a new descendent of Junko and pretends to "reveal" that Junko was behind it all along, going as far as to make several TakeThat[=s=] to this trope's usage in ''Danganronpa'', saying that no matter how predictable or repetitive it is, the mastermind always has to be Junko due to tradition. But in reality, this turns out to just be another lie from Tsumugi.
* In ''VideoGame/DarkSoulsII'' both the FinalBoss of the overall game and the ''Crown of the Old Iron King'' DLC, as well as the first boss of the ''Crown of the Sunken King'' DLC, are all revealed to be the LiteralSplitPersonality of the EldritchAbomination [[OmnicidalManiac Manus, Father of the Abyss]] who was the FinalBoss of the [[VideoGame/DarkSoulsI previous game]]'s ''Artorias of the Abyss'' DLC and responsible for much of the conflict in the game's background.
* In ''VideoGame/DawnOfWarII: Chaos Rising'', Eliphas was revived by Abaddon to serve Araghast as his 2nd in command. But when the Blood Ravens finally defeat Araghast, he leaves him to die, and takes command of the Black Legion forces. In ''Retribution'', it is revealed that the whole assault on the sub-sector Aurelia was orchestrated by the daemon, inadvertently released by Gabriel back in the end of the first game.
* In ''VideoGame/DawnOfWarIII'', what starts off as a war between the Imperium, Orks, and Eldar quickly devoles into a plot about Eldar reclaiming one of their relics to kill a Greater Daemon of Khorne, even though Daemons weren't present in the start of the game. In a post credits sequence it is revealed that the Necrons are also involved.
* Who is and isn't a villain in ''VideoGame/DeusExInvisibleWar'' is subject to some interpretation, but it's a major [[WhamEpisode Wham]] to find out that [=ApostleCorp=] is led by JC Denton, the player character from the original ''VideoGame/DeusEx''.
* The main antagonist of ''VideoGame/DevilMayCry5'' is a giant demon named "Urizen" who is trying to use a demonic tree to become stronger. However, newcomer V seems to have a vague connection to him and late in the game it's revealed that he and Urizen are [[LiteralSplitPersonality two halves of the same being]]: the human and demon side of half-demon Vergil, series protagonist Dante's EvilTwin. With his body decaying since [[VideoGame/DevilMayCry1 his last appearance]], Vergil attempted to separate his humanity from his demon heritage but only managed to tear away his conscience from his lust for power. They eventually recombine and Vergil is restored in the climax.
* Though it was obvious judging by the cover and the title, Diablo turns out to be the real final boss in ''VideoGame/DiabloIII'', despite being apparently dead in the second opus and the third one focusing essentially on demonlords Belial and Asmodean for all the first part of the game.
* In ''VideoGame/DivinityOriginalSinII'', Bishop Alexandar was built up to be the BigBad. Then it turns out he was just a DiscOneFinalBoss (twice) and the ''true'' BigBad is Dallis the Hammer. But then, it turns out that Dallis was a BigBadDuumvirate with none other than RogueProtagonist Lucian. And within the FinalBoss fight with Dallis and Lucian, ''[[EvilOverlord Braccus Rex]]'' (an antagonist from the previous ''Original Sin'' game) emerges as the villain. Then he takes over and becomes the TrueFinalBoss. Larian explained Braccus Rex's presence (and foreshadowed it) with him being BackFromTheDead by necromancy.
* King K. Rool (or, as he preferred to be called in this game, [[MadScientist Baron K. Roolenstein]]) in ''VideoGame/DonkeyKongCountry3DixieKongsDoubleTrouble'' hijacks the antagonist slot from evil robot KAOS...who was, in the end, just a puppet leader for the Kremlings, controlled by him and possessing zero free will.
* ''VideoGame/DragaliaLost'' has this happen in Chapter 12. Prince Euden and Leonidas had been at war with each other when the void dragons, who up to this point have been {{Bonus Boss}}es appear and commanded by Phares, the second Scion.
* In ''[[VideoGame/AnnabelleRPGMaker The Exorcism of Annabelle Sunray]]'', [[SinisterMinister The Preacher]], the new villain who runs [[OrphanageOfFear The Church]] and is trying to keep Annabelle imprisoned, is revealed to be Jason Sunray, Annabelle's abusive father and the antagonist of the first three games.
* ''Franchise/FarCry'':
** ''VideoGame/FarCryNewDawn'' takes place [[LateArrivalSpoiler after the nuclear bombing of Hope County]] at the end of ''VideoGame/FarCry5'', and the main antagonists for most of the game are the [[AnarchyIsChaos Highwaymen gang]], whilst [[SinisterMinister Joseph Seed]] has retired from active villainy. By the end of the game, Joseph's BastardBastard son Ethan betrays New Eden to the Highwaymen, and the [[PlayerCharacter Captain]] fights [[ScaryBlackWoman Mickey and Lou]] there. After that, the next villain to defeat is Ethan, turned into a monster by the mystical apple that gave the Captain their power. After the Captain puts Ethan down, Joseph has a VillainousBSOD and asks the Captain to grant him a MercyKill to atone for all the atrocities he carried out in the name of God. The Captain can either kill Joseph or let him live as CruelMercy.
** Pagan Min from ''VideoGame/FarCry4'' is revealed to still be alive in the ''Control'' DLC of ''VideoGame/FarCry6'', [[VillainProtagonist and is the protagonist.]] [[spoiler: The secret ending implies that he was the one responsible for nuking Montana at the end of ''5'', making him the GreaterScopeVillain of the last two games. [[CuttingOffTheBranches And then there's]] the secret ending of ''Collapse'' [[MindScrew which reveals the nukes never happened to begin with]].]]
* For most of ''VideoGame/DirgeOfCerberus'', Vincent fights the Tsviets, but the true villain of the story is Hojo who was possessing Weiss.
* In ''VideoGame/FireEmblemMysteryOfTheEmblem'', Hardin is the main antagonist for most of the game, but later it turns out that all of his actions and loss of sanity were orchestrated by Gharnef, who in turn seeks to revive Medeus.
* The ''VideoGame/FiveNightsAtFreddys'' franchise: [[BigBad William Afton]] pulls this one in almost every single game, which he even lampshades with his ominous {{catchphrase}} "I always come back."
** ''VideoGame/FiveNightsAtFreddys2'' introduces the new, "Toy" counterparts to the animatronics from [[VideoGame/FiveNightsAtFreddys the first game]]. After about two nights of fending them off, the older ones come out and start hunting down the player's office, far more aggressive than the new ones did. Meanwhile, all of the toy counterparts save for Mangle stop attacking almost entirely until the bonus nights. And if that isn't enough, it's also shown that the Toys are attacking you because of what William has done; As in, either he tampered with the animatronics, or they're haunted by a ''[[ThereIsAnother second]]'' set of victims.
** ''VideoGame/FiveNightsAtFreddys3'' gives us Springtrap, the newest BigBad of the game, [[DistantSequel given that everyone else is dead]]. However, it then turns out that he is possessed by William's undead spirit.
** ''VideoGame/FiveNightsAtFreddys4'' has the Nightmare animatronics. Originally, they seem like they have nothing to do with William, partially because they're dreams. And then the next game comes out and reveals that William has monitored the ''[=FNaF=] 4'' bedroom and might have even created the Nightmare animatronics.
** ''VideoGame/FiveNightsAtFreddysSisterLocation'' shows new, futuristic variations of the Freddy Fazbear gang, as well as some new friends. However, all it takes is ''[[UpToEleven the first cutscene]]'' to reveal they were created by Afton.
** ''VideoGame/FreddyFazbearsPizzeriaSimulator'' has heavily teased Baby, implying she will maintain the BigBad spot from the past game. [[DownplayedTrope And while that is technically true]], she has to share the BigBadDuumvirate with Afton.
** Ok, so that's it, Afton was KilledOffForReal in ''Pizzeria Simulator'' and ''VideoGame/UltimateCustomNight'' is his eternal {{Hell}}. There is no way that he would return in ''VideoGame/FiveNightsAtFreddysVRHelpWanted'' to hijack whoever is the villain this time, [[TemptingFate right?]] Wait, who's that yellow rabbit in the corner and why-Ah, goddamit, [[BackFromTheDead he's at it again]].
** He ''was'' killed off for real, but it was his VirtualGhost terrorizing the company in ''Help Wanted'' who's now [[JackTheRipoff continuing his work through]] [[RogueProtagonist Vanessa/Vanny]], who he [[DemonicPossession possessed]] and is using to once again terrorize children in ''VideoGame/FiveNightsAtFreddysSecurityBreach''. [[spoiler: In the GoldenEnding he gets his body back, only to be trapped in the burning pizzeria ''again'' by [[BlobMonster the Blob]].]]
* In ''VideoGame/FullmetalAlchemist2CurseOfTheCrimsonElixir'', the game's BigBad is a former state alchemist named Crowley who uses an army of alchemical {{Golem}}s throughout the story which he controls through a PhilosophersStone in a ruined nation. In the post-credits scenes, Envy, Lust, and Gluttony talk about the situation, revealing they manipulated Crowley toward finding the stone to bring back his dead lover, although unlike most of their meddling they underestimated Crowley and lost control of the situation. However, they (and as a result likely Dante) still served as the GreaterScopeVillain and the true instigator of the events.
* Zig-zagged in ''VideoGame/GoldenSunDarkDawn'', since the [[TheChessmaster recurring]] [[EvilGenius baddie]] is openly hanging out with the new baddies, in a PaperThinDisguise, for much of the game. However, all the characters believe him to have been dead since [[VideoGame/GoldenSunTheLostAge the last game]], so it's a shock to ''them'' when his identity is revealed. He laughs. And this being Alex, [[HiddenAgendaVillain we still don't even know what he's after]], [[TheUnfought nor do we get to beat him down for it]]. In a sense, it's played straight. At first, it seems like you're going to stop the Psynergy Vortexes and get the roc feather, but the Vortex subplot is dropped after Konpa Cave until TheStinger, and the roc feather quest takes a backseat to stopping the Grave Eclipse.
* In ''VideoGame/{{Ikaruga}}'', the Stone-Like from ''VideoGame/RadiantSilvergun'' is once again the cause of game's troubles, this time having corrupted Horai into a power hungry dictator and granting her unimaginable powers, and is later confronted as the FinalBoss after Tageri is destroyed.
* ''VideoGame/Injustice2'': So after the first ''VideoGame/{{Injustice|GodsAmongUs}}'' ended with them getting their collective rear ends kicked, arrested, humiliated, and now Brainiac and the Legion of Doom are trying to take over and/or kill everything and they are actually forced into an EnemyMine situation with Batman and the other heroes, did you ''really'' think that Superman and the Regime would stop trying to TakeOverTheWorld and turn it into a tyrannical PoliceState [[BewareTheSuperman where they could annihilate anything they considered a threat to peace (or just plain pissed them off) at will]]? Yeah...'''[[{{Determinator}} no]]'''.
* In ''VideoGame/Jak3Wastelander'', it's revealed that [[DragonAscendant Errol]] was turned into a cyborg and is working with the Dark Makers.
* Implied in an ending illustration in ''VideoGame/TheKingOfFighters 2002'' (which was a plotless DreamMatchGame featuring several characters from different story arcs, some of them already dead). Rugal gets to be the final boss in that one, just like in the previous dream match (''KOF '98''), but the illustration curiously shows [[http://www.vgmuseum.com/end/neogeo/c/kof2k2.htm him sitting in a throne surrounded by boss characters from the NESTS Chronicles story arc,]] implying he may have been behind it all. Plausible, as his last canonical appearance in the series (''[='95=]'') had a version of him with cybernetic implants, white hair, and a darker skin tone compared to his previous appearance in ''[='94=]'' -- darker skin and white hair aren't uncommon features of clone characters in the NESTS saga, as isn't cyborg/robotic technology, so the Omega Rugal from ''[='95=]'' could have been a clone, and the real one might still be around. This is given possible support in the console versions of ''XIII'', where Rugal can be seen hacking into the monitors of the ''[=SkyNoah=]'', the CoolAirship of his children Adel and Rose, to keep an eye on them.
* ''Franchise/KingdomHearts'', thanks to its [[MindScrew confusing]] [[KudzuPlot cosmology]], has a rather weird example: the BigBad of the entire series is Xehanort, but he appears in many different incarnations over the series, and these incarnations repeatedly pull this trope on the other villains. The one time he isn't behind things is ''[[VideoGame/KingdomHeartsCoded coded]]''. The rest of the time:
** [[VideoGame/KingdomHeartsI In the first game]], Maleficent was presumed to be the BigBad leading a cabal of Disney villains, until the original villain Ansem was revealed to be the true mastermind manipulating her.
** ''[[VideoGame/KingdomHeartsChainOfMemories Chain of Memories]]'' introduced Organization XIII, which served as the villains of that game and ''[[VideoGame/KingdomHeartsII II]]''. ''II'' revealed that "Ansem" was actually Xehanort's [[TheHeartless Heartless]], and his [[EmptyShell Nobody]], Xemnas, was the leader of Organization XIII, and he served as primary antagonist of both games and the ''[[VideoGame/KingdomHearts358DaysOver2 358/Days]]'' spin-off that takes place in the same time frame. [[note]]Technically, the Organization members in ''[=CoM=]'' were working on their own plan to overthrow Xemnas, but he was still the one that told them to go mess with Sora.[[/note]]
** The prequel ''[[VideoGame/KingdomHeartsBirthBySleep Birth by Sleep]]'' has the elderly Master Xehanort as the main villain, but in the ending he performs GrandTheftMe on Terra, taking over his body to become a new, younger Xehanort, which is the Xehanort that became Ansem and Xemnas.
** ''[[VideoGame/KingdomHearts3DDreamDropDistance Dream Drop Distance]]'' had Ansem and Xemnas return with a new villain, which turned out to be a younger Master Xehanort traveling through time, and all three of them were working on a plan to reform Organization XIII led by a resurrected Master Xehanort commanding them all.
** Promotional materials for ''VideoGame/KingdomHeartsIII'' say that Master Xehanort is the main villain for the game, making it the first time WordOfGod doesn't try to hide his involvement. But ''even then'', the events of ''VideoGame/KingdomHeartsX'' establish two new characters, the Master of Masters and his apprentice Luxu, and heavily implies they have a connection to Xehanort in some manner, so the trope is set to happen once again in some way. It's actually [[InvertedTrope inverted]], Luxu--better known in the present day as [[TheDragon Braig/Xigbar]]--[[TheManInFrontOfTheMan was manipulating Xehanort the whole time]].
** And for the (presumably) final time, in ''VideoGame/KingdomHeartsMelodyOfMemory'' an apparition of Xehanort residing within Kairi's heart serves as the FinalBoss.
* ''Franchise/{{Kirby}}'':
** While not present in the main story, the Dededetour Mode of ''VideoGame/KirbyTripleDeluxe'' reveals that BigBad Queen Sectonia was corrupted into villainy by [[EvilTwin Dark Meta Knight]], TheDragon in previous ''Franchise/{{Kirby}}'' game ''VideoGame/KirbyAndTheAmazingMirror'', via the Dimension Mirror.
** ''VideoGame/KirbyStarAllies'' shows the cloaked figure, Hyness, the clear BigBad, botching a summoning ritual and causing dark hearts to spread across the universe. Throughout the game, the game appropriately builds up the encounter with him, revealing his arsenal, his minions, and his generals before a raid on TheVeryDefinitelyFinalDungeon. However, immediately after a short fight with him where he reveals his true face, he immediately sacrifices himself and his minions to revive his Dark Lord Void Termina, who, while mostly original in appearance, is very heavily implied to be connected to [[VideoGame/KirbysDreamLand2 Dark]] [[VideoGame/KirbysDreamLand3 Matter]].
** In ''VideoGame/KirbyAndTheForgottenLand'' after defeating Forgo Leon, the Soul Forgo leaves his body to fight Kirby right before a familiar butterfly flies on their nose and absorbs their power...and then it brings forth the final final boss of the story: Morpho Knight. It's then subverted as Fecto Forgo then ''survives'' and absorbs Morpho Knight's power, becoming the final final ''final'' boss, Chaos Elfilis.
* In ''Knightfall: Death and Taxes'', it turns out that the Prince of Darkness from the original game is behind the Duke.
* Done retroactively in the ''VideoGame/LegacyOfKain'' series. The first game, ''Blood Omen'', has the BigBad "Hash'ak'gik", while the villains of ''Blood Omen 2'' (actually the [[NonLinearSequel fourth game in the series]]) are the Sarafan, but it's eventually revealed the Sarafan Lord who leads them is a Hylden, a race of beings from another dimension. The fifth game, ''Defiance'', revealed that Hash'ak'gik and the Hylden Lord were the same being all along. He then partially hijacks ''Defiance'' as well, possessing Janos in the penultimate level and revealing that Raziel's game-long search for how to revive Janos is something he had set up.
* ''Franchise/TheLegendOfZelda'': In multiple games, the hot new BigBad turns out to simply be a pawn of [[TropeNamers Ganon]] or to be [[SealedEvilInACan trying to revive him]].
** ''VideoGame/TheLegendOfZeldaALinkToThePast'' features an odd, ambiguous situation as main villain Agahnim is said, depending on the version, to be either a pawn of Ganon or purposely working for him, yet Ganon directly refers to the dark wizard as his own alter ego right before the final battle (which is supported by an image of Ganon's shadow popping out of Agahnim's body, turning into a bat, and then flying into the Pyramid of Power). If such a claim is indeed true, as further hinted by Agahnim's {{Leitmotif}} becoming Ganondorf's theme from ''VideoGame/TheLegendOfZeldaOcarinaOfTime'' onward, Ganon hijacked the game from ''himself''.
** ''VideoGame/TheLegendOfZeldaOracleGames'': The Twinrova sisters, Kotake and Koume, are the real villains, directing the actions of General Onox and Veran in order to resurrect Ganon. Ganon is the FinalBoss, but he does not directly have a hand in the plot, making him more of a GreaterScopeVillain.
** ''VideoGame/TheLegendOfZeldaFourSwordsAdventures'' is an odd mixture of this and TheManBehindTheMan. Vaati is a recurring villain from the prequel game ''VideoGame/TheLegendOfZeldaFourSwords'', and is further established in ''VideoGame/TheLegendOfZeldaTheMinishCap'' which was released after ''Adventures''; but about halfway into the game we find out that Ganon is the true villain of the story, just using Vaati as a decoy. In this case, Ganon hijacks the game from the newer villain Vaati, but Vaati has already been established as a villain as an alternate to Ganon, so Ganon becomes TheManBehindTheMan as well.
** ''VideoGame/TheLegendOfZeldaTwilightPrincess'': After being built up as "The Twilight King" for much of the game, Zant becomes the victim of yet another twist hijack by Ganon. While the appearance of this trope was the cause of debate for years after release, it was already known prior to release that Ganondorf would appear, and the game itself foreshadows (before outright saying) that Ganondorf is the identity of the power-granting god whom Zant reveres.
** ''VideoGame/TheLegendOfZeldaSkywardSword'': Played with in the ending, as while Ganon doesn't appear in any degree due to the game's placement in the series' timeline (long before the first historical appearance of the Gerudo king in ''Ocarina of Time''), the outcome of the FinalBoss battle reveals that the spirit of Ganon, which keeps pursuing Zelda and Link's descendants, is [[HereditaryCurse the incarnation]] of [[ThePowerOfHate the hatred]] of Demise. In short, every single hijacking Ganon does is also a hijacking by Demise.
** ''VideoGame/TheLegendOfZeldaALinkBetweenWorlds'': Zig-zagged. Yuga first appears to be the BigBad, but then Ganon enters the picture, revived by Yuga. Just as you expect him to take the position of BigBad, Yuga absorbs Ganon's power and merges with him before he can do anything, seemingly ''[[DefiedTrope defying]]'' the trope at first. But ''then'', Princess Hilda is later revealed to be [[TheManBehindTheMan The Woman Behind the Man]] all along, and you think Yuga's role as BigBad is going to to stop then and there. Instead, he actually [[TheStarscream betrays Hilda]], turns her into a painting, and absorbs ''her'' power, once again keeping his position. There's also the implication that Yuga is the [[AlternateUniverse Lorule]] counterpart of Ganondorf, meaning that Hilda got hijacked by ''two Ganons at once''.
** ''VideoGame/HyruleWarriors'': Zig-zagged but ultimately played straight in the game. The apparent BigBad at the start of the game is Cia, a corrupted witch and AntiVillain. It's soon revealed that the driving force behind her corruption was none other than Ganondorf himself. However, his initial attempt to hijack the plot is thwarted when he tries to pull a YouHaveOutlivedYourUsefulness on Cia, only for her to turn the tables and banish him with the Triforce. For a while it looks like Cia's going to be the BigBad after all, but Ganon takes advantage of her conflict with the heroes to restore his full power and promptly takes over again after they've dealt with her. In an amusing twist from the usual, the game lets you ''[[VillainShoes play as him]]'' as he performs the hijacking. The game has a bit of a LeaningOnTheFourthWall moment when Ganondorf first reveals himself, as he says Cia was his "favorite puppet yet."
** ''VideoGame/CadenceOfHyrule'':
*** In the main game, played straight between Octavo and Ganon. Octavo is actually trying to ''defeat'' Ganon, to ScrewDestiny and avoid being defeated by Ganon as foretold. His methods [[SelfFulfillingProphecy end up serving the King of Evil's purposes instead]].
*** In Octavo's Ode, the [[ArtifactOfDoom Golden Lute]], the BigBad of the other side of the IntercontinuityCrossover, pulls this on Ganon, turning Octavo into [[VideoGame/CryptOfTheNecroDancer the NecroDancer]] and crushing Ganondorf before he can become Ganon and take over Hyrule. The player, as Octavo's past self, must put the [=NecroDancer=] down.
** ''VideoGame/HyruleWarriorsAgeOfCalamity'' [[PlayingWithATrope plays around with this trope]], but ultimately plays it straight. Harbinger Ganon is a dormant version of Terrako from the new timeline that is corrupted by Malice brought when the Terrako of [[VideoGame/TheLegendOfZeldaBreathOfTheWild the main timeline]] jumped into the past to [[SetRightWhatOnceWentWrong try and change it]], becoming Ganon's vessel in the process. Meanwhile, Astor perfectly knows that he's working for Calamity Ganon, but he sees the Calamity as an extension of himself, lending it the power to destroy Hyrule and then rule the world. When Astor ends up being defeated in the battle in Hyrule Castle, Harbinger Ganon puts him in his place by [[DevourTheDragon quite literally hijacking Astor's body and then using it to form Calamity Ganon itself]], due to Astor's [[YouHaveFailedMe repeated failures]] and [[EvilIsNotAToy having the gall to order Ganon around]].
** Even ''Ganon himself'' isn't immune to being hijacked. In ''VideoGame/SoulcaliburII'', Link's character profile explains that he came to the ''Soul'' universe as a GuestFighter because he discovered that a sorcerer he defeated, very strongly implied to be the ''[[VideoGame/TheLegendOfZeldaOcarinaOfTime Ocarina of Time]]'' incarnation of Ganondorf, was under the influence of [[BigBad the evil sword Soul Edge]].
* ''VideoGame/LittleBigAdventure 2: Twinsen's Odyssey''. Turns out the aliens are just dupes of good ol' Doctor Funfrock.
* In a way, this is played with during the final boss fight of ''VideoGame/MadWorld''. After getting to the final area, you're set to fight the previous champ, and it is never revealed who that is, so one would expect a powerful new face that may reveal something about Jack's past in the games. Then, get ready for this, IT'S THE BLACK BARON. Yes, the guy who died multiple times as a joke character to explain how mini-games work is the final boss and has no clue who Jack is. Oh, and they're surprisingly badass. While the main plot continues as expected, the final boss fight is with the least expected person...but one that has been previously established as a villain of sorts.
* ''VideoGame/MassEffect2'':
** Although it was always pretty obvious, Shepard and co don't confirm the Collectors are working for the Reapers until halfway through the game. Though everyone shrugged and said "It's probably Reapers" in the first conversation about the Collectors. Note that ''VideoGame/MassEffect1'' and ''VideoGame/MassEffect2'' end up presenting the plot twist in the exact same way: by introducing a minor proxy faction as the major antagonist, only for them to turn out and only be a pawn to a greater game. The reveal that the Geth are tools for the Reapers is played up very close to the reveal that the Collectors are tools for the Reapers.
** In a more direct reveal, the main antagonist of ''2'' is Harbinger who is framed as being the Collector General. Only at the end of the game is it revealed that from the very beginning Harbinger was a Reaper which was operating through the General.
* ''VideoGame/MassEffect3'' then follows suit by revealing half-way through that Cerberus and the Illusive Man have become (unwitting) tools for the Reapers as a result of their tinkering with Reaper tech between ''2'' and ''3''.
* After defeating Lord Bane in ''VideoGame/MaximoVsArmyOfZin'', Maximo learns that the title army was awakened by the ghost of King Achille, main villain of the [[VideoGame/MaximoGhostsToGlory first game]].
* This is the trademark tactic for Dr. Wily and Sigma in the ''Franchise/MegaMan'' series.
** Wily pretended to reform in ''VideoGame/MegaMan3'', and in all subsequent main series games except ''VideoGame/MegaMan7'', ''VideoGame/MegaMan8'', and ''VideoGame/MegaMan11'', he turns out to be using the initial villain or some other phenomenon as a decoy. He also does it in ''VideoGame/MegaManV'' for the Game Boy with the Stardroids, though in a bit of a twist, he is ''not'' the final boss of the game. Amusingly, the game doesn't even ''try'' to hide that he's the final boss of ''VideoGame/MegaMan9'' or ''VideoGame/MegaMan10'', as the achievement for beating each game is "Whomp Wily!"
** A lot of fangames that have Wily as the BigBad of the game, like ''VideoGame/MegaManUnlimited'' and ''VideoGame/MegaManSuperFightingRobot'', also go this route, though the latter has Mega Man see this trope coming.
** In the ''VideoGame/MegaManX'' games, Sigma hijacks all the main villains from ''VideoGame/MegaManX2'' onward, to the point it's a twist that he ''isn't'' the BigBad of ''VideoGame/MegaManX8'' (though the plotpoint of New Generation Reploids having Sigma's DNA in their Copy Chips as well as Lumine more or less carrying out Sigma's plans means he's instead a GreaterScopeVillain). This gets {{lampshade|Hanging}}d in ''VideoGame/MegaManX4'' when Split Mushroom responds to a demand to reveal the mastermind behind the game's plot with the [[MemeticMutation meme-tastic]] "Take a wild guess", after which his lifebar, carrying [[GratuitousGreek Sigma's]] [[BroughtToYouByTheLetterS logo]], appears, unlike members of Repliforce. [[note]]Magma Dragoon, Cyber Peacock, and Double also display Sigma's logo, signifying their status as true Mavericks, rather than dudes just trying to gain their independence from the society that's unjustly persecuting them.[[/note]] It's also subverted in ''VideoGame/MegaManX6'', where the BigBad was ''not'' Sigma; it was Gate, and Gate resurrected Sigma to use him to destroy X, but Sigma CameBackWrong (due to stretching himself too thin when he [[VideoGame/MegaManX5 spread the Sigma Virus over the entire planet]]) and was obviously not the controlling force behind the plot. Even so, despite being the Reploid equivalent of a RevenantZombie and only slowly regaining coherence as time passed, Sigma drops this line upon revealing himself and offing Gate in the process.
--->'''Sigma:''' Oh please. I did not die. Nor did I need your help! Now get lost!
** ''VideoGame/MegaManX5'' reveals that the Maverick Virus was originally carried by Zero before it was transferred to and bonded with Sigma, thus meaning Wily hijacked the ''entire'' ''X'' series, because he was the creator of Zero and the original "Zero Virus" that turned Sigma evil. ''X5'' was originally intended to be the final game of the ''X'' series, and WordOfGod has stated that yes, Wily was still alive and was working with Sigma during the game.
** Due to his hand in the creation of the Maverick Virus and Zero, Wily also indirectly set up the events of the ''VideoGame/MegaManZero'' series that acts as a continuation of the ''X'' series, so he could be considered to have hijacked that too, especially when Dr. Weil, the BigBad of the ''Zero'' series, uses a robot (Zero's original body, specifically) that Wily built.
** Dr. Weil himself pulls this off. The [[VideoGame/MegaManZero1 first]] [[VideoGame/MegaManZero2 two]] ''Zero'' games each have different villains, but ultimately Weil (who only first appears in [[VideoGame/MegaManZero3 the third game]]) is the GreaterScopeVillain for both. He even resurrects one of the previous main villains (Copy X) as a PuppetKing and DiscOneFinalBoss, if only to further his plans.
** Finally, the ''VideoGame/MegaManZX'' series that continues the ''Zero'' series, the original Biometal W is a part of the Ragnarok space station from ''[[VideoGame/MegaManZero4 Zero 4]]'' and has Weil's consciousness possessing it, driving other Reploids Maverick. It's also implied to have driven the major antagonists of the games into BrainwashedAndCrazy territory by compelling them to carry out its will. Curiously, Master Albert, the BigBad of ''ZX Advent'' and the person who orchestrated the "Game of Destiny" that drives both games, states that ''he'' is the one in control of Model W and not the other way around. With the ''ZX'' series LeftHanging following Albert's demise, it's unknown if he would've been able to back up his claims, though he does show a far greater understanding and application of Model W's powers compared to Serpent, the main villain of the first ''ZX''.
** In the ''VideoGame/MegaManBattleNetwork'' games (which are an AlternateUniverse from the rest of the series), Wily hijacks ''[[VideoGame/MegaManBattleNetwork2 2]]'' when the main villain of that game reveals in [[VideoGame/MegaManBattleNetwork3WhiteAndBlue the third]] he was working under orders from Wily. ''[[VideoGame/MegaManBattleNetwork4RedSunAndBlueMoon 4]]'' and ''[[VideoGame/MegaManBattleNetwork5TeamColonelAndTeamProtoMan 5]]'' do ''not'' have him, making it actually effective when he appears in ''[[VideoGame/MegaManBattleNetwork6CybeastGregarAndCybeastFalzar 6]]'' and reveals his EvilPlan. However, the villain of ''4'' and ''5'' is the organization Nebula, led by Wily's son.
** Even ''X''-series fangames get in on it. ''VideoGame/MegaManXMavericks'' continues the tradtion of Sigma being behind everything, so there's no point in spoilering it. That being said...
*** In the third game, Sigma is working with Dr. Weil. Sigma ends up getting taken out and Dr. Weil becomes the sole bad guy for the rest of the game. This trope kicks in when after the final battle, we find that Dr. Weil had been possessed...
*** In the fourth game, X is so sure that Sigma is behind Gate's plans that he already starts asking the bosses about it before reaching the fortress. He's right, of course, but Sigma was only brought back thanks to the Stardroids, who were under the leadership of the real bad guy responsible for everything: Dr. Wily.
* A complicated quadruple example in the ''VideoGame/MetalGear'' series. In ''VideoGame/MetalGearSolid2SonsOfLiberty'', Revolver Ocelot (already a villain from ''VideoGame/MetalGearSolid'') reveals himself to be a spy for [[AncientConspiracy The Patriots]], but then gets possessed by the hand of Liquid Snake, the BigBad of ''[=MGS1=]'', and goes rogue. Then in ''VideoGame/MetalGearSolid4GunsOfThePatriots'', Liquid seizes control of the SOP system from The Patriots, becoming the BigBad. Then Ocelot reveals that Liquid wasn't possessing him, and that he was working against The Patriots all along.
* Inverted in the second ''VideoGame/MetalSlug'' game, where [[BigBad Morden]] is hijacked right at the end by the [[TheStarscream Martians]] introduced in that game. Similarly inverted in the fourth game, where the plot appears to be Morden's work but it ultimately turns out to be a robot copy created by a new BigBad unrelated to any of the previous games, and in the sixth game, where the Martians' plot (working once again with Morden) is hijacked by a Martian-eating race of aliens, forcing an EnemyMine between the heroes, the Rebel Army, and the Martians.
* ''Franchise/{{Metroid}}'':
** In ''VideoGame/MetroidPrime2Echoes'', the [[TheHeartless Ing]] are the villains for most of the game, with the player occasionally running into the mysterious Dark Samus. As it turns out, the Ing were being used by Dark Samus, who turns out to be Metroid Prime, the final boss of the first game. She goes on to take the starring role as the BigBad of ''VideoGame/MetroidPrime3Corruption'', making her the overarching villain of the ''Prime'' subseries.
** In ''VideoGame/MetroidOtherM'', the events aboard the Bottle Ship are the fault of MB, who is essentially a resurrected Mother Brain. The postgame is a more jarring and unexpected example. Remember Phantoon? A boss who only appeared in ''VideoGame/SuperMetroid'' and was never heard from again? He takes control of the Bottle Ship in the postgame and, considering the creatures are still out to kill you, he may have helped MB cause the uprising from the background, making him the GreaterScopeVillain.
** In ''VideoGame/MetroidIIReturnOfSamus'', the FinalBoss is the Metroid Queen. In the 3DS remake, ''VideoGame/MetroidSamusReturns'', Samus' nemesis Ridley is tacked on at the end, as a closer tie-in to the chronological followup, ''VideoGame/SuperMetroid''.
* ''VideoGame/MonkeyIsland'':
** Subverted in ''VideoGame/EscapeFromMonkeyIsland'', where after a lot of buildup for the anti-pirate business tycoon Ozzie Mandrill as the new villain, [[BigBad LeChuck]] appears...and it turns out he's working for Mandrill, who really ''is'' the new villain.
** In ''VideoGame/TalesOfMonkeyIsland'', [=LeChuck=] is [[BroughtDownToNormal depowered]] and [[HeelFaceTurn turned good]] at the start of Chapter One, and the Marquis De Singe is built up as the main villain, endlessly pursuing Guybrush so that he can use his unique strain of the Pox Of [=LeChuck=] to create the immortality-granting Jus De Vie. However, at the end of Chapter 4, The Marquis suffers DeathByIrony, and [=LeChuck=] reveals that his "good" act was just that, an act, and ''kills Guybrush''.
* In the ''VideoGame/MortalKombat11: Aftermath'' expansion, it seems that [[TimeMaster Kronika]] is the main villain just like in the main campaign, as she needs to be defeated and her crown retrieved before the timeline can be properly restored. However, thanks to being a ManipulativeBastard and TheChessmaster, longtime villain [[EvilSorceror Shang Tsung]] manages to outsmart everyone and become the BigBad for the first time since [[VideoGame/MortalKombat1 the original arcade game]]: he [[DemotedToDragon demotes his old boss, Shao Kahn, to a Dragon without him realizing it]], [[YourSoulIsMine absorbs Kronika's soul]], and [[GodhoodSeeker uses the crown and hourglass to become the new Keeper of Time]]. It's only thanks to a ''massive'' BatmanGambit from Liu Kang that there's still a chance to stop him, and even '''that''' won't be enough [[TheBadGuyWins if you trigger Tsung's story ending]].
* In ''VideoGame/NarutoClashOfNinja Revolution 2'', the player spends most of the game fighting against Kagura, an evil ex-ANBU agent who wants revenge on Tsunade. It turns out that Kagura was seemingly manipulated into attacking the Hidden Leaf Village by [[TheDragon her Dragon]], Bando, who in turn was manipulated by Kabuto for unknown reasons (it's unclear whether he did it on his own, or for Orochimaru).
* ''VideoGame/NinjaGaiden II'' on the NES spends a lot of time building up Ashtar, the self-proclaimed "Emperor of Darkness," as the BigBad. Your showdown with him occurs only halfway through the game though, and after you kill him, Jaquio, the villain of the previous game, returns from being NotQuiteDead to become the main villain.
* ''VideoGame/{{Oddworld}}: Abe's Exoddus'' features the [[MegaCorp Magog Cartel]] as the primary villains, lead by the [[BigBadDuumvirate Big Bad Triumvirate]] of Vice President Aslik, General Dripik and Director Phleg. Partway through the game, however, it's revealed that Molluck, the BigBad of ''Abe's Oddysee'', was their boss. It's subverted by the fact that he was killed off at the end of ''Oddysee''. Since so little time -- probably a week at most -- passes between the two games, and ''Exoddus'' shows that his [[DragonAscendant ex-Dragons]] are still dealing with the fallout of his death, he was ultimately responsible for everything that takes place in both games, despite not having a direct hand in the sequel's events.
* Zigzagged in ''VideoGame/Persona5Strikers''. The remnants of the Antisocial Force, the main antagonists in ''VideoGame/Persona5'', are the one who hired Akira Konoe, making them responsible for most of the events of the game. The final boss of the game is the Demiurge, which technically makes it different from Yaldabaoth. However, the Demiurge and Yaldabaoth are the same entity in various ideologies, only with a different name.
* ''VideoGame/PhantasyStar'':
** In the first four games, the BigBad revealed early on might be an [[EvilOverlord evil king]], an [[AIIsACrapshoot evil intelligent computer]], a [[HumansAreBastards scorned and now vengeful half-human monster]], a [[WeAreStrugglingTogether fabricated war]] [[CainAndAbel between the heroes']] [[EnemyMine civilizations]], or an [[OmnicidalManiac omnicidal]] EvilSorcerer, but they all ultimately turn out to be pawns of [[EldritchAbomination Dark Force]]. In the fourth game, even Dark Force is revealed to be the millennial incarnation of the [[SealedEvilInACan Profound]] [[UltimateEvil Darkness]].
** When they say that darkness [[ExactlyWhatItSaysOnTheTin cannot be killed]], they aren't kidding. ''VideoGame/PhantasyStarOnline''? Dark Falz. ''Episode II''? Dark Falz' corruption. ''Episode III''? Dark Falz fragments. Move on to ''VideoGame/PhantasyStarUniverse'', and what's the source of the SEED? Dark [[SpellMyNamewithAnS Falkis]]. ''Episode II'', ''III'', and ''Portable'' all have Illuminus essentially side-by-side with Dark Falz. {{Averted|Trope}} with ''Portable 2'', then ultimately played straight with ''Portable 2 Infinity'' and the 108 fragments of Dark Falz. It's not even a surprise when the supposedly defeated Dark Falz ends up returning in ''VideoGame/PhantasyStarOnline2''.
** ''Online 2'' has a much more effective instance later on with ''Episode 3'''s revelation of Dark Falz's progenitor: the Profound Darkness. Completely unlike Falz's constant presence in the series, this is the first new appearance of the Profound Darkness since its debut ''two decades prior''.
* ''VideoGame/PokemonUltraSunAndUltraMoon'' have an interesting variation on this: After completing the game's first half, defeating the Aether Foundation, Lusamine and the Elite Four, the exclusive new story involves [[VideoGame/PokemonRedAndBlue Giovanni of Team Rocket]] literally hijacking the Aether Foundation's headquarters for his newly-established Team Rainbow Rocket...which has the leaders of ''[[Franchise/{{Pokemon}} other]]'' evil teams (taken from parallel dimensions) as high-ranked members.
* In ''[[VideoGame/ProjectXZone Project X Zone 2]]'', the FinalBoss, Byaku Shin, is actually a revived 99, who was originally the true BigBad from ''VideoGame/NamcoXCapcom''.
* ''Franchise/RatchetAndClank'':
** The ''Ratchet & Clank Future'' trilogy builds up a lot of backstory and introduces new villain Percival Tachyon. Tachyon is taken out in the first game, ''[[VideoGame/RatchetAndClankFutureToolsOfDestruction Tools of Destruction]]'', and in the sequel, ''Quest for Booty'', Slag from the last game gets an upgrade to become the new villain. All of that, however, is thrown right out the window when the end of the game reveals that the entire subplot regarding Clank and the Zoni (which turns out to be the ''real'' plot of the game) was actually set up by Dr. Nefarious, from ''[[VideoGame/RatchetAndClankUpYourArsenal Up Your Arsenal]]''. This trope would then be inverted in ''All 4 One'', however.
** In ''VideoGame/RatchetAndClankGoingCommando'', our heroes are offered a job by the CEO of [=MegaCorp=], one of Gadgetron's competitors in the Bogon Galaxy. Their job is initially to recover a stolen prototype, and as the game unfolds, we learn that the CEO is not as kindly as he first appears, and that the prototype will spell doom for the entire universe if unleashed. After fighting their way into his headquarters and confronting him, it's revealed that the CEO was Captain Qwark, the bumbling FakeUltimateHero who served as one of the first game's antagonists, in disguise. Turns out he'd engineered the whole thing in order to save the galaxy from a menace he created in order to be taken seriously as a superhero. Ratchet ends up having to save the galaxy instead after he screws it up.
** ''VideoGame/RatchetAndClank2016'' does this in both game and movie form. A retelling of the first game, one of the many additions to the cast is none other than Dr. Nefarious, who originally hadn't shown up for another two games, and as noted above had become quite a bigger player in the series since. Three guesses what happens...
* Averted in ''VideoGame/ResidentEvil7Biohazard''. The Umbrella Corporation doesn't have anything to do with this incident at all, and in fact their only presence is through a new company called Blue Umbrella, made up of former employees who joined forces with the B.S.A.A. in the intervening years between ''[[VideoGame/ResidentEvil6 6]]'' and ''7'' to [[TheAtoner atone for]] the original company's various wrongs. While the H.C.F. (a task force under the control of Wesker after he split off from Umbrella) is mentioned in files as having collaborated on the project that led to the "birth" of Eveline, it's unknown if Wesker himself, who was KilledOffForReal in ''VideoGame/ResidentEvil5'', had any direct involvement.
* In ''VideoGame/{{Rosenkreuzstilette}} Freudenstachel'', Iris Zeppelin, who instigated the war between RKS and the Church in the first game, is revealed to be behind the Dark Magi and Spiritia's kidnapping, having been posing as the Pope via a [[OurHomunculiAreDifferent homunculus]]. Probably not a huge surprise, considering what [[Franchise/MegaMan this game is a homage to]].
* ''VideoGame/SlyCooper'' subverts this:
** [[VideoGame/Sly2BandOfThieves The second game]] centers around the robotic body parts of previous BigBad Clockwerk, and Sly's attempts to destroy them and make sure he can never threaten anyone again. Clockwerk's body is reassembled in the final level...and it turns out that Arpeggio doesn't want to resurrect the old owl, just use his body to become immortal. Even when Clockwerk comes alive again, it's not his mind in the metal body, but Neyla's. Just to drive the point home, the final scene has Carmelita destroy a vital component that renders Clockwerk DeaderThanDead.
** Clockwerk's appearances in ''VideoGame/SlyCooperThievesInTime'' also subvert this; they have nothing to do with the plot, simply serving as {{Easter Egg}}s to observant players.
* ''Franchise/SonicTheHedgehog'':
** In ''[[VideoGame/SonicRushSeries Sonic Rush Adventure]]'', Eggman and Eggman Nega turn out to be the real threat behind Captain Whisker.
** In ''VideoGame/SonicGenerations'', Modern Eggman and Classic Eggman are controlling the Time Eater.
** DoubleSubverted in ''VideoGame/SonicLostWorld''. After losing control of the Deadly Six, he is forced to work with Sonic and Tails. Once the group is defeated, Eggman returns as the final boss.
* In Steve Meretzky's ''[[VideoGame/TheSpellCastingSeries Spellcasting 201]]'' (an InteractiveFiction game published by Legend Entertainment), the villain of the game turns out to be the villain of the previous game, ''Spellcasting 101'', (the evil stepfather of the protagonist) in disguise. The same trick is pulled in the sequel, ''Spellcasting 301'', and it's done with an even more heavy-handed joke: it turns out that the father disguised himself as a ridiculously hot woman. Talk about having it in for your son...
* In ''VideoGame/SpiderManPS4'', for most of the game you're fighting against Mr. Negative, a relatively obscure Spider-Man villain (having been first introduced in ''ComicBook/BrandNewDay''), with the threats of Mayor Osborn merely looming over Peter's civilian life, until Peter's close friend, business partner, and ParentalSubstitute Otto Octavius starts losing his mind over his deteriorating physical health and getting increasingly aggressive in his anger at Osborn, until he finalizes his life's work: [[ComicBook/DoctorOctopus a set of powerful robotic limbs and a mind altering cyborg implant to control them]]. Immediately after, the Sinister Six are assembled.
* ''VideoGame/StarFoxAdventures'': Andross ends up hijacking General Scales, and his power is the main reason why Scales managed to amass so much power and influence to become the tyrannical ruler of Sauria in the first place. You even have to beat him the same way as in ''VideoGame/StarFox64''. The hints foreshadowing Andross' return are scarce (due to the game's difficult development cycle), but they exist.[[labelnote:Namely...]]During the game's prologue, Andross kidnaps Krystal, who manages to see the perpetrator's identity shortly beforehand (it obviously wasn't Scales, as he stayed in his galleon after Krystal confronted him). Later in the game, Andross (still as a spirit) watches over Fox's progress in one of the Krazoa tests (Fear). And one of the Cheat Tokens, when deposited into the well of the Maze, hints that Andross is still present in some way in the Lylat system.[[/labelnote]]
* ''VideoGame/StarTrekOnline'':
** It's revealed that, ultimately, the real BigBad was the Iconians, whom ''Series/StarTrekTheNextGeneration'' established as being long extinct. Not only are they not, they are behind most, if not all, of the big conflicts in the game leading up to their defeat. They are even responsible for the Hobus supernova that destroyed Romulus and kickstarted the Kelvin timeline.
** The Dominion are responsible two foes touched upon in the television franchise and who make their grand appearance in the game: firstly the Hur'q who were once a peaceful civilisation turned mindless berserkers, because they were the Dominion's first failed experiment in creating drug-addicted super soldiers; the second enemy are the Fek'Ihri horde, who were the second botched attempt by the Founders to make a subservient soldier race out of the Klingons aeons ago.
* Emperor Tenebrae/Vitiate/Valkorion in ''VideoGame/StarWarsTheOldRepublic''. As the leader of [[TheEmpire the True Sith Empire]] he serves as the BigBad for the game and the GreaterScopeVillain of the [[VideoGame/KnightsOfTheOldRepublic Old Republic]] saga overall. However, after being defeated by the [[PlayerCharacter Hero of Tython (Jedi Knight class)]] he returns as the GreaterScopeVillain of the ''Shadow of Revan'' expansion before coming [[BackFromTheDead back to life]] for the ''Eternal Throne'' and ''Fallen Empire'' expansions to serve as the BigBad for those. He's finally KilledOffForReal in the ''Onslaught'' expansion after ''four'' attempts within the same game.
* ''Franchise/SuperMarioBros'': Bowser tends to take centerfold whenever he's not the BigBad of some games.
** In ''VideoGame/SuperMarioSunshine'', it turns out he's the father of Shadow Mario, a.k.a. Bowser Jr. But Bowser doesn't appear until the final level and acts as the final boss even though Bowser Jr. was the main recurring enemy for the entire game.
** Bowser has been doing this since he was baby, taking over the main antagonist spot from Kamek in ''VideoGame/SuperMarioWorld2YoshisIsland''. However, this doesn't prevent adult Bowser himself from making surprise appearances in some of the ''Yoshi's Island'' games as well. ''VideoGame/YoshisNewIsland'' has him [[GiantSpaceFleaFromNowhere bending space-time]] just to become the FinalBoss of the game, meaning that he hijacks ''his own younger self''.
** Averted, but attempted in ''VideoGame/PaperMarioTheThousandYearDoor'', where Bowser is not the main antagonist. He and Kammy Koopa appear in several cutscenes seeking the [[StarShapedCoupon Crystal Stars]], but always arrive after Mario and company have left with the Stars. In the climax, Bowser drops in...[[DynamicEntry literally]]...during the confrontation between Mario and Grodus (the essential main antagonist), and then the player has to fight Bowser and Kammy. But once the player defeats Bowser and Kammy, it turns out that Grodus took advantage of the distraction to grab Peach and take her to the next chamber. So in the end, Bowser doesn't hijack the plot. He never even finds out what's going on, and ends up being little more than comic relief in the otherwise serious endgame.[[note]]To push Bowser's humiliation even further, his post-Grodus fight is also the ''only'' boss fight in the game that is '''not''' immune to [[OneHitKill Showstopper]]. So, not only does Bowser not get any meaningful interactions with the overall plot, ''he doesn't even get ContractualBossImmunity like every other boss.''[[/note]]
-->'''Bowser:''' What's a finale without a Bowser appearance, huh? A cruddy finale, that's what!
** In ''VideoGame/MarioAndLuigiPartnersInTime'', Bowser isn't the BigBad. Once the battle against The Shroobs is finished, Bowser becomes the PostFinalBoss after being given a power boost.
** In ''VideoGame/MarioAndLuigiDreamTeam'', the supposed BigBad, Antasma, forms an [[BigBadDuumvirate alliance]] with Bowser, but Bowser, under the impression that Antasma was planning to betray him (and uninterested in sharing victory with him anyway), betrays Antasma ''first''.
** ''VideoGame/LuigisMansion'' subverts this. The game implies about 3/4 of the way through that Bowser is going to hijack the plot. At the end of the game, the final boss, King Boo, flies into a Bowser portrait and sucks Luigi in, teleporting him to the roof of the mansion, where Luigi is pitted against what appears to be Bowser. However, "Bowser" is revealed to be nothing more than a hollow puppet being controlled by King Boo. Bowser himself has no part in it.
** In ''VideoGame/LuigisMansionDarkMoon'' plays with this trope as well. Luigi and Professor E. Gadd don't know who broke the Dark Moon, end up fighting off a bunch of Possessors, and only in the last mansion realize that recurring villain King Boo was behind everything. [[DramaticIrony The player, on the other hand, knows this from the start.]]
** In ''VideoGame/DanceDanceRevolutionMarioMix'', the first world sets Waluigi up as a main antagonist for the first time ever, then Wario and ''then'' Bowser jack the later parts of the plot.
** ''VideoGame/MarioPlusRabbidsKingdomBattle'' zig-zags the trope. The game sets up Bowser Jr. as the main antagonist, only for both him and the player characters to find out that Bowser will be coming home early. By the time the player reaches Bowser's Castle, Bowser has been defeated and possessed by the Megabug that was a constant yet ignored presence throughout the entire game.
* ''VideoGame/SuperRobotWars'':
** [[Characters/SuperRobotWarsAlpha Euzeth Gozzo]]. In ''VideoGame/SuperRobotWarsAlpha'', the player is led to believe [[Characters/SuperRobotWarsAlpha Laodecia Judecca Gozzo]] and [[Characters/SuperRobotWarsAlpha Ingram Prisken]] are the {{Final Boss}}es, but Euzeth enters and states the former two serve him, making Euzeth the actual endgame opponent. In the ''[[VideoGame/SuperRobotWarsOriginalGeneration Second Super Robot Wars Original Generation]]'', Euzeth returns via MesACrowd through his AlternateUniverse proxy [[Characters/SuperRobotWarsOriginalGeneration Arteil Steinbeck]] and usurps the FinalBoss to become the TrueFinalBoss of the game.
** In ''VideoGame/EndlessFrontier'', there's a whole lot of new characters and villains, but [[VideoGame/SuperRobotWarsCompact2 The Einst]] are the real enemies.
** In ''VideoGame/SuperRobotWarsCompact2'', specifically in ''Impact'' after obtaining enough Battle Masteries, the TrueFinalBoss of the game goes from fighting [[EldritchAbomination Neue Regisseur]] to fighting ''[[Anime/MobileSuitGundamCharsCounterattack Char Aznable in the Sazabi]]''. [[SugarWiki/AwesomeMusic Cue]] ''[[https://www.youtube.com/watch?v=58gIsVJ7NuQ Beyond the Time]]''.
* ''VideoGame/SuperSmashBros'':
** Although Master Hand is the flagship FinalBoss in the series, it subverts this trope in [[VideoGame/SuperSmashBrosBrawl The Subspace Emissary]]. After Bowser, Wario, and the Ancient Minister have been causing most of the trouble, Ganondorf is revealed to be in charge of them behind the scenes. However, Ganondorf is himself taking orders from Master Hand, only to find that [[TheBigBadShuffle yet another villain was controlling Master Hand the whole time]].
** Used in [[VideoGame/FinalFantasyVII Sephiroth's]] reveal trailer for ''VideoGame/SuperSmashBrosUltimate''. It opens with the assembled fighters attempting to fight back against Galeem, the BigBad from the game's story mode. However, just as it's about to launch a final attack, it suddenly gets sliced in half. The monster disintegrates, revealing Sephiroth to be its killer; he then assaults the fighters, going after [[ArchEnemy Cloud]] in particular.
* In ''VideoGame/SystemShock2'', you initially believe that The Many is the BigBad, having hijacked the Von Braun's crew with mind control. Then your MissionControl turns out to be SHODAN from the previous game. After you wipe out The Many, SHODAN becomes the villain, though the [[SpoilerOpening box art and intro]] might have given it away. This is partly because ''[=SS2=]'' was meant to be a new standalone game, with the ''System Shock'' elements bolted on afterwards.
* In ''[[VideoGame/TimeCrisis Time Crisis: Project Titan]]'', Ricardo Blanco is set up to be the BigBad, being the one responsible for framing Richard Miller for assassinating the president of Caruba, Xavier Serrano, but after defeating Ricardo, [[TheDragon Wild Dog]] comes in and [[TheStarscream kills Ricardo]], making Wild Dog the true BigBad of ''Project Titan''.
* ''VideoGame/TronTwoPointOh'': Okay, so we have Thorne causing massive viral outbreak all over cyberspace, [[UnwittingPawn but he's only a patsy of F-con]], who wants to use the Shiva laser to upload an army of human mercenaries to conquer the Program world. With F-con, Seth Crown appears to be the one in charge, [[TheManBehindtheMan but...wait, there's the F-con CEO above him!]] Emails you download during the course of the game hint that F-con's CEO is actually Edward Dillinger from the first ''Film/{{Tron}}'' film! [[note]] WordOfGod from Monolith said it was Dillinger, at least. But there's also a possibility that, like in ''Film/TronLegacy'', a resurrected Master Control Program is posing as Dillinger [[/note]]
* Boss Cass, the BigBad in ''VideoGame/TyTheTasmanianTiger 1'' and ''2'', is presented as TheQuisling (though, like [[Webcomic/EightBitTheater Black Mage]], this would imply he'd never been on "Team Evil") with [[TheHeartless the Quinkan]] in ''Ty 3''. He's the one who invited them over for a nice cup of tea and a spot of global domination.
* ''VideoGame/ValkyrieProfile2Silmeria'' is hijacked at the end by Lezard Valeth, who had been a party member for most of the game, thus giving the impression he was a different person entirely from [[VideoGame/ValkyrieProfile the first game's]] incarnation. Turns out that the only reason he exists in that timeline is that he decided to use a time travel device to go back, so that he can steal the power of Silmeria and Odin and become powerful enough to do what he wanted to do in the first place -- steal Lenneth Valkyrie's soul and force her to merge with him.
* With no real buildup [[note]]he appears on the box art, and that's it[[/note]], Carnage randomly appears as the final boss of ''Venom/Spider-Man: Separation Anxiety'' (sequel to ''Spider-Man and Venom: Maximum Carnage'') for SNES/Sega Genesis.
* In ''[[VideoGame/VirtuaCop Virtua Cop 3]]'', the leader of the terrorist organization is revealed to be none other than Joe Fang, who was thought to have been killed twice.
* ''VisualNovel/VirtuesLastReward'':
** Nine individuals are placed in a Nonary Game, similar to [[VisualNovel/NineHoursNinePersonsNineDoors the first game]], except instead of the person Zero, they are now being watched over by an A.I. rabbit named Zero III. As it turns out, both Zero III and his creator, the future Sigma Klim, are working with the original Zero, Akane Kurashiki. The game attempts to persuade the player early on that this isn't the case, with characters commenting on how the first Zero already got what they wanted.
** In addition, the other antagonist, Dio/Left, is revealed to be a member of the same cult that Ace/Gentaro Hongou, one of the villains of the original game, was from.
* In ''VideoGame/Wasteland2'' the TrueFinalBoss is [[AIIsACrapshoot the Base Cochise A.I.]], the BigBad from [[VideoGame/{{Wasteland}} the first game]] that [[RobotMaster Matthias]] was trying to resurrect and [[EvilIsNotAToy ended up getting controlled by]].
* ''VideoGame/{{Warcraft}}'' pulls this with the Burning Legion. The Legion is behind everything bad that happens in all three strategy games, one way or another. Similarly, the Legion is what ties together many of the plot threads in Classic ''VideoGame/WorldOfWarcraft'', though that game also sets up the threat of the [[EldritchAbomination Old Gods]]. ''VideoGame/WarcraftIII'' subverts it, as the Lich King becomes un-hijacked and the Legion's attempt to re-hijack him fails.
* ''VideoGame/WorldOfWarcraft'':
** The TrueFinalBoss of the ''Burning Crusade'' expansion is Kil'jaeden the Deceiver, one of the arch-demon lords of the Burning Legion and the mover behind most of the events of the expansion. However, his appearance in the final content patch came as a surprise to almost everyone, since all of the promotion for ''BC'' was focused on the confrontation with Illidan. Even the mighty Kael'thas Sunstrider was seen as something of a throwaway boss -- a stepping stone to Illidan -- until it was revealed that he was acting as a SycophanticServant for Kil'jaeden.
** The ''Warlords of Draenor'' expansion started with a time-travelling Garrosh convincing his father to ''reject'' the demonic influence of the Burning Legion. The players must travel to this alternate timeline and fight back against the orcs' new Iron Horde, which is stronger than ever due to them imprisoning the Legion's emissary Gul'dan and embracing superior technology instead of fel magic. However, the expansion somehow ends up with Gul'dan back on top and the players battling the demonic hordes yet again. This continued into the following expansion, Legion.
* In ''[[VideoGame/AeroTheAcroBat Zero the Kamikaze Squirrel]]'', the mastermind behind Jaques Le Sheets' scheme is Edgar Ektor.
* The story of ''VideoGame/DungeonMaster 2: The Legend of Skullkeep'' appears to be completely unrelated to that of the original game, until the cinematic at the very end that reveals that Chaos, the villain from the original game, is really behind it all.
[[/folder]]

[[folder:Live-Action TV]]
* ''Series/ThirdRockFromTheSun'' gives a humorous example. Dick is outraged when he discovers Mary has been getting love letters from a mysterious admirer, and discovers that it's actually his ArchEnemy Liam, who seduced Mary and tried to destroy Earth once before and is back to give both another shot.
* In the final season of ''Series/TwentyFour'', the Russians, who were behind the deaths of Omar Hassan and Renee Walker, were hijacked by Season 5's BigBad, [[PresidentEvil Charles]] [[ManipulativeBastard Logan]]. Season 7 had teased Logan pulling this by constantly referencing him and having Tony go on a RoaringRampageOfRevenge, but unfortunately, it turns out that some [[GiantSpaceFleaFromNowhere random guy]] named Alan Wilson was Tony's target and the one behind multiple conspiracies.
** Also, in The Game, Max, the man behind Season 2's events, is the BigBad.
** Subverted in season six; it seems like the Chinese are pulling this, but Phillip Bauer turns out to be the actual antagonist.
** In the ''Live Another Day'' miniseries, Cheng Zhi returns and pulls this properly, taking over the BigBad position from hacker Adrian Cross almost immediately after he appeared to step into it.
* ''Series/AgentsOfSHIELD'': In a major bit of ArcWelding with the main Franchise/MarvelCinematicUniverse, the first season's villain organization "Project Centipede" is revealed to be a branch of HYDRA.
* ''Series/{{Angel}}'': Lindsey works alongside his lover, Eve, to play Angel and Spike against each other, with the hope of usurping Angel's position at the firm and (if we're aiming high) buying his way into the Circle of the Black Thorn.
* In four out of eight seasons of ''Series/{{Arrow}}'', a seasonal BigBad is revealed to have some connection to the League of Assassins.
* ''Series/BuffyTheVampireSlayer'':
** It turns out the source of various nasty events happening around and to Buffy's circle of friends, not to mention the forces of good around the world, are the work of The First, who appeared in Season 3 as a MonsterOfTheWeek and is now the final villain of the show.
** In the Season Eight comics, it turns out Twilight is actually Angel
** Dark Willow reappears in the ''Time of Your Life'' arc of Season 8.
* Happens in the fifth season of ''Series/{{Chuck}}''. Clyde Decker is set up at the beginning of the season to be operating a conspiracy by a faction of the CIA intent on destroying Chuck Bartowski, his friends, and his family. Midway through the season it's revealed that Daniel Shaw, who underwent a FaceHeelTurn halfway through the third season and tried to take over the CIA before the team stopped him, has been pulling Decker's strings (via blackmail over Decker's corrupt past) all along. And then ''that'' gets hijacked by Quinn, who it's revealed was behind ''everyone'' Chuck had been dealing with out of spite because Chuck "stole" the Intersect from him (Quinn was selected to be the Intersect agent, but after Bryce stole it and sent it to Chuck, Quinn was sent into the field without it, captured, and tortured. Yes, there was a bit of SanitySlippage involved).
* In the denouement of Season 12's events on ''Series/CriminalMinds'', we learn of a ''twofold'' version of this. The main villain at large during this season is Scratch, a psychopath who uses drugs to induce hypnosuggestion in others so that they do his dirty work for him. Halfway through the season, Dr. Spencer Reid gets framed for murder and imprisoned after being drugged in the same way. However, someone is actually replicating Scratch's M.O. down to the letter to make it appear to be him. This someone turns out to be the daughter of a father the BAU was forced to kill for refusing to stand down, having come out of Witness Protection and flipped her lid; she, in turn, is being used by someone else who wants revenge on Spencer for lying to her about her own father just to get her arrested, and who has gone ''absolutely starkers'' from solitary confinement and taken so many levels of crazy that she decided to subject Spencer to the same type of torture in the prison environment.
* The majority of new villains introduced on ''Series/DaysOfOurLives'' in the past 15 years have been revealed to be working for Stefano Di Mera.
* One loses track of how many ''Series/DoctorWho'' serials open with a seemingly original villain who turns out to be a pawn of the Daleks, the Cybermen, the Sontarans, or the Master. Or sometimes more than one of them (and sometimes they hijack each other). The production team would later admit that they overdid it in the eighth series (which introduced the Master), making him the primary villain in ''all five serials.''
** For the first four episodes of [[Recap/DoctorWhoS6E3TheInvasion "The Invasion"]], Tobias Vaughn appears to be the BigBad: He makes coy references to "allies" and is clearly hatching out ''something'', but he seems to be the one driving the plot. Then it turns out that what he's hatching out are Cybermen, who quickly prove to be the bigger threat.
** [[Recap/DoctorWhoS10E3FrontierInSpace "Frontier in Space"]] does it ''twice'': the Ogrons are quickly revealed to be working for the Master (in Creator/RogerDelgado's last story before his death), who turns out in the final episode to have been working for the Daleks.
** In the fourth-episode cliffhanger of [[Recap/DoctorWhoS15E6TheInvasionOfTime "The Invasion of Time"]], the Vardans are defeated...and then it turns out that they were tools for the Sontarans, who turn up to take matters into their own hands.
** Subverted in [[Recap/DoctorWhoS23E4TheUltimateFoe "The Ultimate Foe"]], in which it turns out that the Master was responsible for the events that led to Earth's devastation and the Doctor's trial...and then the Valeyard, a completely new villain, turns out to have taken advantage of the Master's actions to set himself up as the story's real BigBad.
** In Series 1, it turns out the Daleks were leading the Mighty Jagrafess into manipulating the Human Empire's population. Subsequently, they were behind the Gamestation's gathering of humans for their deadly game shows. Then the Cybermen hijacked Torchwood, the Master hijacked Harold Saxon (by ''being'' him), and the Cybermen, Daleks, Sontarans, and a few others hijacked the Pandorica. Yup, still going strong.
** In Series 7, the Great Intelligence being behind everything would count as this. Turns out the villains in [[Recap/DoctorWho2012CSTheSnowmen "The Snowmen"]] and [[Recap/DoctorWhoS33E6TheBellsOfSaintJohn "The Bells of Saint John"]] were just TheDragon to him.
** In Series 8, it turns out that Missy is short for "Mistress" — she's the Master, come back [[JokerImmunity yet again]].
** Another double example in [[Recap/DoctorWhoS36E11WorldEnoughAndTime "World Enough and Time"]], where the creepy patients are revealed to be early incarnations of the Cybermen — and it turns out the Master is responsible.
** Done twice in Series 12 of the new show. Firstly, the villain of [[Recap/DoctorWhoS38E1E2Spyfall Spyfall]] is revealed to be the Master using the identity of [=MI6=] agent O in Part 1. Then the Master turns up again to literally hijack Ashad's plot in "The Haunting of Villa Deodati/Acension of the Cybermen/The Timeless Children".
** {{Spinoff}} ''Series/{{Class|2016}}'' had a huge example at [[Recap/ClassS01E08TheLost the end]] of its first [[CutShort and only]] season — the Governors are an apocalyptic PathOfInspiration working for the Weeping Angels.
* ''Series/TheFlash2014'':
** In Season 5, the BigBad is the metahuman SerialKiller Cicada. However, in the last episodes of the season, it's revealed that Eobard Thawne the Reverse-Flash has been faking his apparent atonement, and that ''the entire season'' was a BatmanGambit to manipulate [[KidFromTheFuture Nora]] into altering the timeline enough that he could escape his execution in the future. When this succeeds with Cicada's defeat in the season finale, Thawne serves as the FinalBoss of the season.
** The ''Armageddon'' storyline in Season 8 sees alien psychic Despero travelling back in time to kill Barry Allen because Despero believes that Barry will cause a cataclysmic event in 2031 (the time period when Despero came from). However, once Barry travels to that future to see for himself, the man responsible is once again Eobard Thawne, who orchestrated a "Reverse-Flashpoint" where he replaced Barry Allen as the Flash in history and turned the entire world against him.
* The second, third, and fourth volumes of ''Series/{{Heroes}}'' were hijacked by Sylar, who, while not the mastermind of the first volume, was the unwitting means to Linderman's end, and much more deadly. The volumes set up their BigBad as, in order, Adam Monroe, Arthur Petrelli, and Emile Danko, only for them to be dealt with a couple episodes before the end of the volume, generally unceremoniously. Sylar's MO is to pop out of nowhere at around that time and catch everyone with their pants down, brewing some mayhem for an episode or two until the heroes get him under control...at least until the next volume begins.
** This is made all the more predictable by each volume's insistence on having a major plot thread centering around Sylar regaining his powers, deciding he'd rather be evil, or remembering who he is.
** Ultimately subverted in the final volume, where Samuel Sullivan is established as the BigBad fairly early on and keeps that title right up until the finale. Not only does he [[CurbStompBattle easily defeat]] Sylar the one time they fight, but Sylar has a HeelFaceTurn that actually seems to ''stick'' this time.
* ''Franchise/KamenRider'':
** Whenever the series pulls off a MassiveMultiplayerCrossover, you can be sure that the [[Series/KamenRider series' original]] NebulousEvilOrganisation, Shocker, would have its name all over the plot.
** In the Showa era, Shocker's Great Leader was either directly behind or revealed to be secretly puppeteering most of the evil organizations the Kamen Riders faced. It's easier to list the organizations he wasn't behind, that being Dogma and Jin Dogma in ''Series/KamenRiderSuper1''[[note]]Although ''Manga/KamenRiderSpirits'' alludes to the Great Leader having a connection to them as well, the manga is non-canon[[/note]] and Gorgom in ''Series/KamenRiderBLACK''[[note]][[Series/KamenRiderBlackRX The Crisis Empire]] doesn't have any ''official'' connection to the Great Leader, but it's a popular fan theory that Emperor Crisis is, in fact, another incarnation of the Great Leader, due to having the same voice actor, states that he had fought the 10 previous riders personally sometime in the past, and shares a "big floating head" appearance that the Great Leader's last appearance, [[Film/KamenRiderZX The Great Leader of Badan]], had[[/note]]. He's for the most part stopped hijacking the plot in the Heisei era, but whenever there's a [[LegionOfDoom gathering of villains]], nine times out of ten it's him who's leading the charge.
** It seems ''Series/KamenRiderDouble'', ''[[Series/KamenRiderOOO OOO]]'', and ''[[Series/KamenRiderFourze Fourze]]'' are getting hijacked by Foundation X, as they were involved with the {{Transformation Trinket}}s of each season in some way.
* ''Franchise/SuperSentai''
** In ''Series/TokusouSentaiDekaranger vs. Series/BakuryuuSentaiAbaranger'', the villain's plot was revealed to be to resurrect not only all the Alienizers and Trinoids that have been slain in battle, but Dezumozorlya (the Abarangers' EldritchAbomination BigBad) as well. Fortunately, it was the dead [[SixthRanger AbareKiller]] who was resurrected in Dezumozorlya's stead, and Killer proceeds to team up with his fellow Sentai to defeat the various villains.
** It is played straight, however, in ''Series/EngineSentaiGoOnger vs. Series/JukenSentaiGekiranger'', the villains are after the Dōkokugan, the sphere that the Gekirangers' BigBad Long is sealed in, and he later breaks free of the seal in order to exact his revenge.
* In ''Series/{{Lost}}'', the first antagonist encountered in the series is the Smoke Monster, which had been terrorizing the survivors since they first crashed on the Island, long before we even know about the Others. Early on, it was assumed that it was a raging beast, but later, we learned it was much more than that when it was discovered that it could assume the form of deceased characters. However, it only appeared in a few episodes and seemed to take a backseat to other antagonists such as Ben, the Others, Widmore, etc. After seasons of debating who the BigBad would be, the season five finale introduced an unnamed man, The Man in Black, who is Jacob's enemy, vowing to kill him, and at the end of the episode, we learn he was manipulating everyone, especially Ben and Locke, the whole time in order to accomplish this. It is revealed in the season six premiere that this man was none other than the Smoke Monster, making him the BigBad since the very first episode.
* During the ''Series/{{Monk}}'' season 6 finale, "Mr. Monk is on the Run", Monk is accused of murder and escapes captivity, hoping to prove his innocence. Monk soon figures out that Sheriff Rollins, the very officer that arrested him and has been in pursuit ever since, is the actual murderer, and further investigation leads Monk to discover a conspiracy masterminded by his nemesis Dale "[[FatBastard The Whale]]" Biederbeck.
* At the end of season 4A of ''Series/OnceUponATime'', after Literature/TheSnowQueen [[RedemptionEqualsDeath sacrifices herself to undo her curse]] in the penultimate episode, Rumpelstiltskin takes over as the main antagonist for the final episode and continues this role into the second half of the season with various other previously seen and new villains along the way.
* Evox, the BigBad of ''Series/PowerRangersBeastMorphers'', is revealed to be an reincarnation of a previous series BigBad, specifically Venjix, the BigBad of ''Series/PowerRangersRPM''.
* ''Series/ResurrectionErtugrul'' has this happen in season 4. While he has no direct connection to most of the villains that showed up in the season beforehand, but Baiju Noyan’s (The [[BigBad antagonist]] of season 2) presence near the end comes as a surprise both to the viewers and to Ertugrul and his alps.
* In the ''Series/RobinOfSherwood'' episode "The Enchantment", the witch Lilith turns out to be the girlfriend of Simon de Belleme, the black magician who was the villain of the show's first episodes, and her true objective is to resurrect him.
* The first series finale to ''Series/{{Sherlock}}'' reveals a certain someone to have been behind every mystery ([[BritishBrevity all three of them]]) up to that point, in some way or another. The same happens in episodes 1 and 3 of series 2. He wasn't behind any of the events of series 3 (likely due to his being dead), but he does reappear at the end of the series 3 finale, in such a way to [[JokerImmunity make everyone doubt whether he actually died at all]].
* The Granada adaptation of the Series/SherlockHolmes mystery "The Red-Headed League" ultimately connects its mastermind with Holmes' nemesis Moriarty. No such connection exists in the original story. However, the real-life crime that inspired "The Red-Headed League" was masterminded by the man who inspired Moriarty.
* In ''Series/TheAdventuresOfSherlockHolmesAndDoctorWatson'', the three episode arc concerning Moriarty starts with an adaptation of "The Adventure of Charles Augustus Milverton", who apparently was part of the gang, since Holmes caught the Professor with the help of some documents the bastard had.
* ''Series/StargateSG1'':
** In season 3, Sokar, the Goa'uld who the show had been building up as the new BigBad since the previous season, was unceremoniously killed in a 2-parter and his forces were taken over by Apophis, who was revealed to [[DeathIsCheap still be alive]].
** In season 8, Ba'al takes control of Anubis's remaining forces after the destruction of Anubis's fleet during the invasion of Earth, and uses his superior [[SuperSoldier Kull Warriors]] to successfully [[EnemyCivilWar wage war on all the other Goa'uld combined]]. Anubis reappears on Earth, but gets stuck on a frozen planet in a dying host body. At the end of the first part of "Reckoning", Ba'al reveals to O'Neill that Anubis is back in command of the largest Goa'uld faction, and that he was serving him for a while now.
* ''Franchise/StarTrek'':
** In the ''Series/StarTrekTheNextGeneration'' episode "Descent", the rogue Borg the ''Enterprise'' has been chasing turned out to be led by [[EvilTwin Lore]].
** In ''Series/StarTrekDeepSpaceNine'', an episode investigating the Orion Syndicate has a big reveal that they have been working for the Dominion.
* The conclusion of ''Series/TinMan'' reveals that the BigBad [[GodSaveUsFromTheQueen Princess Azkadellia]] is actually a descendent of [[Literature/TheWonderfulWizardOfOz Dorothy Gale]] and was possessed by the spirit of the original Wicked Witch as a child. D.G. (who's actually Azkadellia's sister) frees her from the Witch's influence in the last episode's final act, and she reverts to her original personality.
* In one episode of ''Series/TheTwilightZone1959'', a neo-Nazi campaign is hijacked by a mysterious phantom who delivers excellent advice on public speaking. It turns out that the phantom is none other than UsefulNotes/AdolfHitler. When Hitler reveals his identity to the neo-Nazi leader, he stops giving advice and starts giving orders.
* In the tokusatsu series ''Series/UltramanNexus'', there is a constant reference of "The Unknown Hand" being the mastermind behind everyone of the Space Beasts actions, as well as reoccurring baddie, Dark Mephisto. Once the final monster is destroyed, the unknown hand reveals himself to be an entire evil Ultra known as "Dark Zagi".
* The miniseries of ''Series/TheXFiles'' seems to have the Cigarette Smoking Man returning BackFromTheDead and as the BigBad once again.
[[/folder]]

[[folder:Mythology and Religion]]

[[folder:Anime & Manga]]
* ''Anime/BatmanNinja'': The climactic battle involves Gorilla Grodd revealing that he had turned all of the Batman villains that travelled with him to the past into [[ManchurianAgent Manchurian Agents]] that would subconsciously create individual parts of a SteamPunk HumongousMecha that they would then hand over to him so he would TakeOverTheWorld...a plan that worked perfectly okay, [[SpannerInTheWorks except that it turns out]] ComicBook/TheJoker shook off the mind control very early and so he appears with a new part that allows him to take over the mecha, which he will use to raise apocalyptic levels of hell on Japan [[ForTheEvulz for fun]].
* In ''Manga/CodenameSailorV,'' some of this happens once ''Manga/SailorMoon'' begins to run concurrently. Suddenly the Dark Agency was a branch of the Dark Kingdom all along.
* ''Manga/Cyborg009'':
** The majority of antagonists can be traced back to the Black Ghost organization. This is [[LampshadeHanging lampshaded]] in the ''Manga/{{Devilman}}'' {{crossover}} when Cyborg 002 correctly guesses that the High-Teen Number Cyborgs are assassins sent by Black Ghost.
** In the 2001 anime, Skull, the leader of Black Ghost, seemingly dies halfway through the first season. In the "Yomi Kingdom" arc in the second season, it is believed that Van Vogt has become the new leader of Black Ghost. It is later revealed that Skull was still alive and leading the Black Ghost the entire time, and Van Vogt was only the [[TheDragon second-in-command]] of Black Ghost.
* ''Anime/DigimonAdventure02'' has Vamdemon/Myotismon who manipulated Oikawa into the apparent BigBad of the series who in turn, manipulated Ken into the Digimon Emperor, the villain of the first half of the season. The [[AllThereInTheManual video games and a little mention in Tamers]] give this even more of a MindScrew. The Dark Spore which made Ken the Digimon Emperor came from an attack used by Milleniumon. But Milleniumon is a Jogress Shinka[[note]]DNA Digivolution[[/note]] of a dying Khimeramon and Mugendramon.[[note]]Machinedramon[[/note]] [[StableTimeLoop Khimeramon was created by Ken while he was the Digimon Emperor]], so Ken actually created his own hijacker while he was hijacked.
* Played with in the Android Saga of ''Anime/DragonBallZ'': Freeza and his father King Cold appear to the main villains at the very beginning, but they're instantly killed by Trunks who warns them of the real threat: the artificial humans created by Dr. Gero, a former member of the original series' villains The Red Ribbon Army, and whose cyborg Cell serves as the main villain. Gero, however, never made any appearance, nor was he ever mentioned in the original arc.
* The manga based on the ''VideoGame/GalaxyAngel'' gameverse changed the entire plot of ''Moonlit Lovers'' so that Eonia, who was [[UsefulNotes/SchrodingersCat already dead in the game]], could be behind it again.
* ''Manga/GetterRobo'' has the Dinosaur Empire, which acted as the main antagonists of the original manga. In ''Go'', the antagonist is initially the MadScientist Professor Lando, but it's then revealed that he's allied himself with the Dinosaur Empire, and in later chapters, the Empire pulls a coup, revealing that he was never truly in control of his army.
* ''Anime/GodMars'' has President Gihron of Marmelo as the BigBad of its second arc. He is advised by a mysterious voice that claims he is destined to rule the galaxy. The voice sounds a lot like Zuul, the Big Bad of the first arc. During the final confrontation with Giron, the voice reveals he ''is'' Zuul, who has returned to continue his war against the main character, killing Gihron in the process.
* In the ''Franchise/DanganRonpa'' SpinOff series ''Manga/KillerKiller'', it's shown early on that SerialKillerKiller Takumi became the way he is after witnessing a mass murder at his middle school, with the culprit supposedly still being on the loose. About halfway through it's revealed that the killer was none other than [[PosthumousCharacter Mukuro Ikusaba]], who's been [[VisualNovel/DanganronpaTriggerHappyHavoc long since dead by the time the manga began]].
* The ''Manga/HeavensLostProperty'' manga introduces a new evil Angeloid called Siren...who gets killed in about 3 pages by earlier villain [[CreepyChild Chaos]], who then absorbs her powers. Ow.
* In ''Manga/TheKindaichiCaseFiles'', if the murderer of the week sets up a more elaborate plot than usual, there's a good chance that he/she employed the "services" of Yoichi "The Puppeteer from Hell" Takato, ArchEnemy of series protagonist Hajime Kindaichi. There are also a few ReverseWhodunnit cases where it's clear that Takato is the one pulling the strings, but Hajime still has to figure out the actual murderer.
* An in-universe example in ''Manga/MyHeroAcademia''. We're told for the majority of the series that Tomura Shigaraki has been groomed by All For One from a young age to take his place as The Symbol of Evil. This is supposedly because All For One's body is failing him after his battle with All Might left him half-dead with permanent injuries. Shigaraki has All For One (the superpower, not the man) surgically implanted into his body. This allows All For One to pull a GrandTheftMe on Shigaraki, as it turns out every quirk has the user's consciousness imprinted on it.
* ''Manga/{{Naruto}}''
** Orochimaru does this during part one of the anime's interminable filler seasons — they even retcon Mizuki, from the first chapter, into having been operating under the orders of Orochimaru.
** Zig-zagged with Akatsuki. First it was revealed that it was all the doing of Jiraiya's former student by name Nagato. But wait, it was actually Tobi, who calls himself Madara but actually he is Obito Uchiha and it was actually real Madara, who manipulated him to resurrect him so he could become god. But wait, later we learn that Obito never had any intention of reviving Madara and himself using him in order to become god. But then, rather abruptly, it's revealed that Black Zetsu is doing this to ''both of them''. In fact, he's been manipulating everything connected to the Uchiha and Senju clans since before their founding as part of a ploy to resurrect Kaguya. This includes leading Madara and Obito around by the nose (including somehow ''tricking Madara into thinking he had created Zetsu''), starting Akatsuki and having Kabuto discover Madara's body.
* In ''Manga/{{Inuyasha}}'' it's almost inevitable that whoever the heroes are fighting next is really a pawn of [[BigBad Naraku]]. However, to their credit, the heroes are almost always aware of this, increasingly so as the series goes on. And then it turns out Naraku was being manipulated all along by the Shikon jewel -- and the [[GreaterScopeVillain ancient dragon youkai]] inside of it.
* Guile Hideout, the ArcVillain of the ''Emerald'' chapter of ''Manga/PokemonAdventures'', is later unmasked to be Archie of Team Aqua, who survived the events of the ''Ruby and Sapphire'' chapter. And his armor was given to him by Sird, an EnigmaticMinion previously affiliated with Team Rocket during the ''[=FireRed and LeafGreen=]'' chapter.
* The US dub of ''Anime/PokemonHeroes'' made Annie and Oakley agents of Team Rocket when in the original they had no association with them.
* ''Anime/PuellaMagiMadokaMagica'''s SpinOff ''Manga/PuellaMagiKazumiMagica''. [[ChekhovsGunman And everyone thought Kyubey's appearence was just a cameo...]]
* In ''Anime/PuellaMagiMadokaMagicaTheMovieRebellion'', Kyubey also reveals himself as being responsible for the plot, after having spent the first part of the movie pretending to be a harmless mascot. Ironically, at the end of the movie, he himself is hijacked by ''Homura'' of all people!
* Dr. Wily manages to pull one of these off in ''Anime/MegaManNTWarrior''. The 2 beast viruses, Grieger and Falzer, are the BigBad for the majority of the series until it's revealed that a dead, and reduced to digital form, Dr. Wily programmed and released them on purpose to let 1 kill and absorb the other, thereby creating the ultimate body for him to download himself into.
* A key plot element in ''VisualNovel/UminekoWhenTheyCry'', also inverted:
** Most of ''End of the Golden Witch'' involves Battler trying to keep the role as protagonist and Bernkastel doing the hijacking.
** In addition, one of the main villains, and the one who gave Beatrice her powers in the first place, Lambdadelta, is shown in a bonus scene to be the one who caused the events of [[VisualNovel/HigurashiWhenTheyCry the previous story]]; and the BigBad of Higurashi, Miyo Takano, is heavily hinted to be a human incarnation/AlternateSelf of Lambda. Ryukishi has denied this, [[TrollingCreator but you never know with him]].
* In ''Manga/ZatchBell'', Riou serves as the main villain for the Faudo arc -- until Zeon and Dufaux invade the control room and absolutely crush him. And it happens right after Riou defeats Gash and [[OnlyMostlyDead murders Kiyomaro]], too.
* ''Manga/AssassinationClassroom'':
** [[SadistTeacher Akira]] [[DrillSergeantNasty Takaoka]] is revealed to be the mastermind in the Assassination Island arc, being the one responsible for infecting half of Class 3-E and demanding Nagisa to surrender Koro Sensei to him.
** Shiro, who is the most frequently recurring villain in the series with the most attempts at killing Koro-sensei, is upgraded to full on BigBad status with the reveal of his true identity of Yanagisawa, the mad scientist who turned Koro-sensei into a tentacle monster and is indirectly responsible for the moon being destroyed and the death of Aguri.
* In ''Manga/FairyTail'', the Alvarez Empire is built up as far stronger and far more evil than anything Fairy Tail has ever faced -- such an insurmountable force that Makarov disbands the guild rather than face them. However, we later find out that the Emperor of the Alvarez Empire is Zeref, and he is the personal cultivator of this empire from scratch — not because he wants to conquer the world, but because he's hoping that it will put him in a position to bring down Acnologia, a true rotten-to-the-core villain.
* Episode 8 of ''Anime/PhantasyStarOnline2TheAnimation'' reveals that many of the bad things happening are the result of (yet again) another Dark Falz, who is using Darkers to seek out Earthlings that possess high Photon affinity. By kidnapping these Earthlings, it hopes to use one as a vessel to manifest itself and invade Earth. Casra, Quna, and Aika have been working behind the scenes to thwart Dark Falz's plans, and now Itsuki needs to be in on it as well.
* ''Manga/SailorMoon'':
** Sailor Galaxia is the BigBad of the fifth and final arc, but the one who drove her actions was the Death Phantom, the BigBad of the second arc.
** [[TheManBehindTheMan Chaos]]. All the main antagonists, except Sailor Galaxia, were agents of his (albeit unknowningly). So basically Chaos is the main instigator of all the events of the manga. Also, while Galaxia isn't an UnwittingPawn of Chaos like the previous main villains, she's actually TheStarscream of Chaos and joined him willingly. This, and the fact that Chaos was the aforementioned Death Phantom, means that Chaos also hijacked the last arc anyway.
* The ''Phantom Bullet'' arc of ''LightNovel/SwordArtOnline'' has the heroes fighting Death Gun, a virtual SerialKiller. It’s eventually revealed that the Death Gun avatar is controlled by ex-Laughing Coffin member [=XaXa=], a.k.a. Shouichi Shinkawa.
* ''Anime/{{Symphogear}}'' seems to like subverting this trope:
** The second season implies that Fine will be the ultimate BigBad again, but when she finally appears, she immediately does a HeroicSacrifice for the good guys.
** ''GX'' has Dr. Ver reappear suddenly, but the current BigBad quickly betrays him, so he also ends up pulling a HeelFaceTurn and HeroicSacrifice. (Fine apparently reappears in ''GX'' and [[FaceHeelTurn has returned to team evil]], but she doesn't last very long or overshadow the current BigBad.)
* In ''Manga/ViolenceJack'', which takes place in the ''Manga/{{Devilman}}'' universe, it is eventually revealed that the Slum King is Demon Lord Zenon, who along with the whole world was recreated by Ryo Asuka aka {{Satan}}. They both become the dual FinalBoss. Also inverted in that the titular protagonist turns out to be a reincarnated Akira Fudo.
* In ''Anime/YattermanNight'', a sequel series to the original ''Anime/{{Yatterman}}'', the BigBad is Lord Yatterman, the leader of the New Yattermen who took over after the death of Dokurobey, the villain of the original series and leader of the Doronbo Gang, and a KnightTemplar who imposes a brutal dictatorship on the people and fights against the new Doronbo Gang to prevent another rise of evil. Until Episode 10 reveals that “Lord Yatterman” ''is'' Dokurobey himself, having survived and taken over the Yattermen with the intention of turning them into a brutal dictatorship, destroying their reputation in the process, as revenge for all his past defeats.
[[/folder]]

A subtrope of ObviousVillainSecretVillain. Might be the result of the new villains managing to ResurrectTheVillain or the old villain being a ReturningBigBad. Inverse of MakeWayForTheNewVillains, and contrast NotMeThisTime. See also DiabolusExNihilo, and TheManInFrontOfTheMan.

''Keep in mind that this is about {{plot twist}}s,'' '''''so EXPECT SPOILERS.'''''

!!Examples:

[[folder:Anime and Manga]]

[[folder:Film — Animation]]

[[folder:Film — Live-Action]]

** [[TheManBehindTheMan Chaos]]. All the main antagonists, except Sailor Galaxia, were agents of his (albeit unknowningly). So basically Chaos is the main instigator of all the events of the manga.

** In ''VideoGame/KirbyAndTheForgottenLand'' after defeating Forgo Leon, the Soul Fecto leaves his body to fight Kirby right before a familiar butterfly flies on its nose and absorbs it...and then it transforms into the true final boss of the story: Morpho Knight. It's then subverted as Fecto Forgo then ''survives'' and absorbs Morpho Knight's power, becoming the true final boss, Chaos Elfilis.

* In ''Anime/YattermanNight'', a sequel series to the original ''Anime/{{Yatterman}}'', the BigBad is Lord Yatterman, the leader of the New Yattermen who took over after the death of Dokurobey, the villain of the original series and leader of the Doronbo Gang, and a KnightTemplar who imposes a brutal dictatorship on the people and fights against the new Doronbo Gang to prevent another rise of evil. Until Episode 10 reveals that “Lord Yatterman” ''is'' Dokurobey himself, having survived and taken over the Yatterman with the intimo of turning them into a brutal dictatorship, destroying their reputation in the process, as revenge for all his past defeats.

An subtrope of TheManBehindTheMan, where an old villain is behind a new one.

A subtrope of ObviousVillainSecretVillain. Might be the result of the new villains managing to ResurrectTheVillain or the old villain being the OverarchingVillain of their setting. Inverse of MakeWayForTheNewVillains, and contrast NotMeThisTime. See also DiabolusExNihilo, and TheManInFrontOfTheMan.

* In ''Franchise/{{Danganronpa}}'', OverarchingVillain Monokuma/Junko Enoshima will turn out to be the real mastermind even in games which appear to have a different antagonist, which is impressive considering she died in the first game.

While still a valid trope in other media, in video games, it's on its way to becoming [[DiscreditedTrope increasingly difficult to take seriously]]. Due to just how ubiquitous the twist is, it's often seen as an overused and trite way of attempting a shocking plot twist (with the trope-naming ''[[Franchise/TheLegendOfZelda Zelda]]'' series and other game series like ''VideoGame/{{Mega Man|Classic}}'' and its follow-ups such as ''VideoGame/MegaManX'', which likewise [[StrictlyFormula used the trope ad-nauseum]], being by far the most infamous abusers of this) that it's no longer considered even mildly surprising to use in contemporary games. Modern games tend to avoid the trope save in series where it's [[GrandfatherClause practically expected]] (such as the aforementioned ''Mega Man'' series) and tend to either play the villains straight, [[TheUntwist subvert the twist]] or [[LampshadeHanging play the cliche for laughs]].

* In ''VideoGame/SolCresta'', it's later revealed that [[BigBad Mandler]], who was also the FinalBoss of ''VideoGame/TerraCresta'' 1 and 2, is once again leading Mega Zofer against humanity despite having thought to be destroyed by Terra Cresta years ago, and that the Mega Zofer generals are using the Vaikun to resurrect Mandler once again.

* In ''VideoGame/DarkSoulsII'' both the FinalBoss of the overall game and the ''Crown of the Old Iron King'' DLC, as well as the first boss of the ''Crown of the Sunken King'' DLC, are all revealed to be the LiteralSplitPersonality of the EldritchAbomination [[OmnicidalManiac Manus, Father of the Abyss]] who was the FinalBoss of the [[VideoGame/DarkSoulsI previous game]]'s ''Artorias of the Abyss'' DLC and responsible for much of the conflict in the game's background.

** In ''VideoGame/KirbyAndTheForgottenLand'' after defeating Forgo Leon, the Soul Fecto leaves his body to fight Kirby right before a familiar butterfly flies on its nose and absorbs it...and then it transforms into the true final boss of the story: Morpho Knight!

* ''Anime/BatmanNinja'': The climactic battle involves Gorilla Grodd revealing that he had turned all of the Batman villains that travelled with him to the past into [[ManchurianAgent Manchurian Agents]] that would subconsciously create individual parts of a SteamPunk HumongousMecha that they would then hand over to him so he would TakeOverTheWorld...a plan that worked perfectly okay, [[SpannerInTheWorks except that it turns out]] ComicBook/TheJoker shook off the mind control very early and so he appears with a new part that allows him to take over the mecha, which he will use to raise apocalyptic levels of hell on Japan.