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[[quoteright:350:[[Franchise/TheLegendOfZelda http://static.tvtropes.org/pmwiki/pub/images/HijackedByGanonC_6941.jpg]]]]
[[caption-width-right:350:What? Were you expecting someone else?\\
[[VideoGame/TheLegendOfZeldaTwilightPrincess Maybe that Zant guy?]]]]

->'''Prologue:''' Hey! Did you know that in the last game there was this nutty computer that tried to kill everyone?\\
'''Yahtzee:''' No, I did not know that. Why did you bring it up?\\
'''Prologue:''' [-errrrmmm, no reason.-] Here's a totally unrelated plot. Also try not to look at the box art.
-->-- ''WebAnimation/ZeroPunctuation'', ''VideoGame/SystemShock2''

An inverted form of TheManBehindTheMan. Rather than a new evil being behind an old villain, an old villain is behind a new one.

This is common for iconic villains (such as many of the ones from Creator/{{Nintendo}} games) with JokerImmunity -- no matter how many times the hero beats them, they keep coming back in the next game. Frequently, they even retry the same evil plot.

Another variant on this trope is when the new villain has no connection to the old one but the old one manages to dethrone the new one and take over as the main villain.

This can be a [[SubvertedTrope subversion]] of OutsideContextProblem, in that the Outside-Context Problem (the original) is actually subordinate to a villain who is ''not'' outside context. Similarly, it could be that the original Outside-Context Villain is not actually the BigBad, but instead the replacement. See also GreaterScopeVillain, where the greater evil is an OutOfFocus entity that has only an indirect effect on the plot.

Nothing to do with HijackedByJesus.

Inverse of MakeWayForTheNewVillains, and contrast NotMeThisTime. See also TheManInFrontOfTheMan, which is another inversion of the TheManBehindTheMan trope.

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



[[folder:Anime & Manga]]
* 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/{{Cyborg 009}}'':
** 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.
* ''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.
* The ''Manga/HeavensLostProperty'' manga [[spoiler: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.]]
* ''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 [[spoiler: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 pretty much 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. [[spoiler:And then it turns out Naraku was being manipulated all along by the Shikon jewel -- and the [[GreaterScopeVillain ancient dragon youkai]] inside of it.]]
* 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''. [[spoiler:[[ChekhovsGunman And everyone thought Kyubey's appearence was just a cameo...]]]]
* In ''Anime/PuellaMagiMadokaMagicaTheMovieRebellion'', [[spoiler: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, [[spoiler:he himself is hijacked by ''Homura'' of all people]]!
* [[spoiler:Dr. Wily]] manages to pull one of these off in ''Anime/RockmanEXEBeast''. The 2 beast viruses, Grieger and Falzer, are the BigBad for the majority of the series until it's revealed that [[spoiler: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 [[spoiler:inverted]]:
** Most of ''End of the Golden Witch'' involves [[spoiler:Battler trying to keep the role as protagonist]] and [[spoiler:Bernkastel]] doing the hijacking.
** In addition, one of the main villains, [[spoiler: 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 [[spoiler: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 -- [[spoiler:until Zeon and Dufaux invade the control room and absolutely crush him]]. And it happens right after [[spoiler:Riou defeats Gash and [[OnlyMostlyDead murders Kiyomaro]]]], too.
* In ''Manga/AssassinationClassroom'', [[spoiler:[[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.]]
* 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 [[spoiler:disbands the guild rather than face them]]. However, we later find out that the Emperor of the Alvarez Empire is [[spoiler:a villain we already know quite well, 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 [[spoiler: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.]]
* ''Anime/SenkiZesshouSymphogear'' seems to like subverting this trope:
** The second season implies that [[spoiler:Fine will be the ultimate BigBad again, but when she finally appears, she immediately does a HeroicSacrifice for the good guys.]]
** ''GX'' has [[spoiler: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.)]][[/folder]]

[[folder:Comic Books]]
* 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.]]
* ''ComicBook/TheAvengers'' robotic villain Ultron has this as pretty much his trademark plot. In every single issue he EVER shows up in, he ''never'' appears to be the main antagonist the Avengers will be up against, rather evidence will point it to being someone else, before Ultron dramatically reveals himself. Even in his very first appearance as a villain, he wore a disguise and diverted suspicion to Jarvis of all people (successfully at that) before it was revealed it was he.
* ComicBook/NormanOsborn's revival at the end of ComicBook/TheCloneSaga definitely counts. We in the real world know he was brought in because the story had long since gotten out of hand, and the best way to resolve it neatly was to have one mastermind behind everything. Osborn, a notorious {{Chessmaster}}, was judged the only Spidey villain with the oomph to pull it off (even if they had to bring him back from the dead).
* ''ComicBook/TheDeathOfSuperman'' did this with its final storyline ''Reign of the Supermen'', the story starts out normally with the first two issues of each title attempting to endear us to the four Supermen. Then come the halfway point of the third month when [[spoiler:the Cyborg Superman decides to ventilate the Eradicator and allow Coast City to be destroyed by Mongul. Then, it turns out the Cyborg Superman was actually a very minor character who was an {{expy}} of [[ComicBook/FantasticFour Reed Richards]]!]]
* A flaw in the later seasons of the ''ComicBook/ElfQuest'' series is that the main villainess Winnowill turns out to be the one behind the machinations for ''every single plot''. Shards? Yeah, that was her, shapeshifted. Wavedancers? Yup, her again. Forevergreen? Oh look, it was her insane minion. Hidden Years? Guess who made all those mutant monsters? It gets old. In the [[CanonDiscontinuity distant future]], residual taint from her evil magics at Blue Mountain is the focus of a major subplot.
* In ''ComicBook/{{Grendel}}'', [[spoiler:Pope Innocent XLII, the BigBad of the 26th century arc, turns out to be Tujiro, the vampire serial killer from the 21st century arc.]]
* The bizarre, surreal, and hilarious -- as with everything else in the book -- reveal of the Comte de Rochefort as the ManBehindTheMan in Jason's ''The Last Musketeer''.
* ''Century: 1969'', the penultimate volume of ''ComicBook/TheLeagueOfExtraordinaryGentlemen'', ends with the revelation that the BigBad Oliver Haddo survived his confrontation with the League by escaping to the astral plane and possessing the body of a young [[Literature/HarryPotter Thomas M. Riddle, aka Voldemort]] (the most well-known literary villain of the 21st century). Sure enough, ''Century: 2009'', the final installment, has the League facing off against Haddo inhabiting Voldemort's body.
* During the "Dead End Kids" arc, the ComicBook/{{Runaways}} end up in New York City in 1907. While there, they are told that the criminal underworld is supposedly run by Maneater (a sort of predecessor to the Kingpin) and the Sinners. Chase and Xavin later discover that the Sinners are actually answering to [[spoiler:Dale and Stacey Yorkes, the parents of Chase's dead girlfriend, and enemies to the Runaways. They are understandably displeased when they find out that Gert's dead in the present day...]] The series also had an attempted Ultron hijack at the beginning of the second volume, but [[spoiler:his attempt to frame Doctor Doom fails and he gets blown up by Darkhawk]].
* In the ''ComicBook/SinCity'' tale ''Hell And Back'', [[spoiler:Wallenquist was revealed as the Colonel's boss, with the Colonel's main assassin answering directly to him]].
* Rastapopoulos makes a few surprise return appearances as the BigBad in a few ''ComicBook/{{Tintin}}'' albums (although not as many as fans seem to think).
* In ''ComicBook/UltimateMarvel'', Dr. Doom has pulled this '''twice''' to date: in [[spoiler:the ''Ultimate Power'' miniseries and in ''ComicBook/TheUltimates'' vol. 3 '']]. Which is weird, because he doesn't have nearly as much cred as his [[MarvelUniverse 616]] counterpart, and except for those two instances, no one besides the Fantastic Four has dealt with him... but there you have it. The former kind of worked, the latter... [[AssPull not so much]].
* This also happened in the 'Master of Doom' story arc of the 616 Fantastic Four title. The Marquis of Death, who had appeared to have killed Dr. Doom and usurped his power early on in the story, was eventually deposed by his own protege, who happened to be... Dr. Doom, who had [[UnexplainedRecovery somehow]] survived the Marquis' earlier attempt to kill him.
* GreenLantern Rebirth: The [[GiantSpaceFleaFromNowhere newly introduced Parallax Entity]] was directed by Sinestro.
* ''ComicBook/TheChildrensCrusade'' retroactively paints Doctor Doom as the one behind the Scarlet Witch going insane, leading to ''ComicBook/AvengersDisassembled'' and ''ComicBook/HouseOfM''.
* In ''ComicBook/BatmanEternal'', [[spoiler:fairly minor villain Cluemaster is revealed as the BigBad of the story who united Batman's RoguesGallery to take down Batman once and for all. However, just as the final battle is about to begin, Lincoln March (who had been serving as Cluemaster's financial backer) sneaks up behind Cluemaster, slits his throat, and hijacks the plot. Lincoln March not only wanted to be the one who killed Batman, but also felt that Cluemaster was missing the point of his own scheme (Cluemaster wanted to be known as a big name villain for his Magnum Opus EvilPlan, which kind of defeated the purpose of concealing his role so thoroughly) and so decided to [[InvokedTrope invoke this trope]].]]
* In ''Comicbook/MickeyMouseComicUniverse'', the Phantom Blot sometimes does this, since he's a DiabolicalMastermind with a penchant for working from behind the scenes as either a HiddenVillain or a ManBehindTheMan. In one story, Mickey offered his services as a detective to a movie producer who seemed to be bothered by aliens. It turned out the whole thing was really a conspiracy by his various employees against him for being such a JerkAss, but the Phantom Blot was the one running the show. (He wanted to stop the making of a movie based on true events in which he had lost to Mickey.) In another, old story, the Blot was in prison, but the antagonist was an EvilGenius who Mickey suspected right away, and correctly, to be one of the Blot's subordinates. In a third story, the ''old'' villain Black Pete was acting really strangely while going out robbing things even though he was supposedly demonstrably in prison. It turned out the Blot had hypnotised both Pete and the prison warden as a RedHerring as part of a bigger plan.

[[folder:Fan Works]]
* In Part 2 of ''FanFic/ClashOfTheElements'', the [[spoiler:[[VideoGame/MarioAndLuigiBowsersInsideStory Dark Star]] appears to be doing this]], but it is {{subverted|Trope}} a couple chapters later when [[spoiler:Chaos Alex regains control of his body from him]].
* While not technically an example, this trope is referenced in the {{Crossover}} ''[[http://forums.spacebattles.com/threads/fate-stay-hijacked.237641/ Fate/Stay Hijacked]]'' [[spoiler:by Ganon]].
* Twice in ''Fanfic/MyBravePonyStarfleetMagic'', in fact. Towards the end of "Season 1", Nightmare Moon is built up as the final antagonist, when suddenly Titan reappears. [[spoiler:He then returns in "TheMovie", hijacking the role of main villain from Distraught.]]
* Even in [[FanFilm fan-films]], Ganon is true to form. ''[[WebVideo/TheLegendOfZeldaTheSageOfDarkness The Sage of Darkness]]'' has an original villain: Etregun, who is a descendant of Ganon. [[GrandTheftMe Guess what happens?]]
* Double subverted in ''FanFic/PerfectionIsOverrated''. Near the end of the fic, the Usurper, in a last bid at defeating the Himes and ruling the world, possesses the Obsidian Lord, who had initially seemed to be the final antagonist the Himes would face. When the Usurper's remaining minions are defeated and the Obsidian Lord is forced out of Reito's body, the Obsidian Lord breaks free of the Usurper's control, killing him, before having one last confrontation with the Himes.
* Played with in ''WebVideo/SonicZombie''. Silver's debut in ''Diaries 3'' has him get hijacked by a new monster antagonist near the end. Then in ''Vengeance'', he comes out of nowhere and interrupts Sonic and Knuckles's fight to steal both of their then-powers and become a OneWingedAngel. His monster form there is the main antagonist. Then in ''Shopping Mall'', he turns out to be the true identity of Metal Sonic, but towards the end a transformed Bowser ends up taking the title of the final villain the heroes have to face. The series being [[StylisticSuck made bad on purpose]], this is all played for laughs.
* Princess Jody, the BigBad of ''[[http://alaxr274.deviantart.com/gallery/33810717 Super Milestone Wars,]]'' becomes the TrueFinalBoss in ''[[http://alaxr274.deviantart.com/gallery/36864527 Super Milestone Wars 2.]]''
* ''WesternAnimation/TotalDrama'' fan season ''FanFic/TotalDramaLuxuryTour'' briefly sets up Alejandro, who was the BigBad of the season immediately before it, as the main antagonist for the first few chapters. Then he's voted off pretty early thanks to Noah, and for the majority of the story following that, Duncan is geared towards being the villain. And ''then'' Alejandro simply ''bribes'' his way back on the game, [[TookALevelInJerkass takes a serious level in jerkass]], and takes over as the main villain, especially after Duncan himself is eliminated near the end.
* ''FanFic/TheEquestrianWindMage'' actually [[InvertedTrope inverts]] this in regards to the {{Trope Namer|s}} -- while Ganon is the main apparent threat in Season 2, it's only because [[GreaterScopeVillain Majora's]] followers engineer his awakening in Equestria instead of Hyrule so that A) he'll be out of their way, B) he'll serve as a distraction to Equestria's heroes, and C) they will deal with him and eliminate the competition for them. Also, it's repeatedly mentioned that Ganon is ultimately just a puppet of Demise's reincarnated hatred. [[spoiler:During the FinalBattle, Demise is resurrected out of Ganon, acting as the TrueFinalBoss.]]
* ''FanFic/WarAndPeaceInMind'': With [[{{Technopath}} Royal Pain]] locked up, the hero community turn to the AcademyOfEvil she already had in place as their main crisis target, along with its secretive Headmaster. [[spoiler:When the heroes finally meet him, it turns out Royal Pain had made an ArtificialIntelligence in her own likeness to run the school.]]
* The ''WesternAnimation/AdventureTime'' fanfic ''FanFic/TheCitadelOfTruth'' sets Astrum up as the BigBad of the fic with The Lich being defeated and turned into one of the Shards Of Evil early on. But once Astrum makes his HeelFaceTurn, all of a sudden The Lich turned out be alive and quite well as he proceeds to hijack the plot and becomes the FinalBoss of the fan fiction.

[[folder:Films -- Animation]]
* Occurs in ''Anime/FinalFantasyVIIAdventChildren''.
** While it wasn't surprising, as Sephiroth was heavily featured in promotional materials, he didn't show up until the last 15 minutes of the movie to hijack it from the Remnants (bonus points for quite literally hijacking Kadaj's body in the process).
** Also in the compilation, ''VideoGame/DirgeOfCerberus''. Vincent fights the Tsviets, but the true villain of the story is [[spoiler:Hojo possessing Weiss]]. Bonus points again for a literal hijacking.
** The entire compilation turns Hojo into this. With Sephiroth receiving a sympathetic backstory and Hojo being the direct or indirect cause of much of the plots, he's honestly the real big bad.

[[folder:Films -- Live-Action]]
* In ''Film/CaptainAmericaTheWinterSoldier'', [[spoiler:HYDRA has actually been resurrected amongst SHIELD's ranks ever since the agency's own formation, the mastermind this time being the Red Skull's right-hand man in ''Film/CaptainAmericaTheFirstAvenger'', Arnim Zola]]. This also puts into light certain events in the ''Film/IronMan'' films, such as the deaths of Tony's parents and Senator Stern wanting to get his hands on Tony's tech. [[spoiler:The former is actually a MakeItLookLikeAnAccident engineered by HYDRA (since Howard Stark was one of SHIELD's founders) while Stern is in fact one of many HYDRA agents.]]
* ''Film/XMenFilmSeries'':
** ComicBook/{{Magneto}} pulls it twice in the films.
*** In ''Film/X2XMenUnited'', he works with the X-Men without much protest or animosity to save mutant-kind, [[spoiler:but once he foils Stryker's plan, he reminds us that he is the BigBad of the series and turns Stryker's Cerebro on normal humans]].
*** In ''Film/XMenDaysOfFuturePast'', [[spoiler:he hijacks the Sentinels to try and kill both Bolivar Trask ''and'' UsefulNotes/RichardNixon. The other BigBad from the movie, Mystique, stops him]].
** In ''Film/TheWolverine'', [[spoiler:Ichirō Yashida was alive all along and was the real mastermind behind weakening Wolverine and kidnapping Mariko. Shingen was nothing in the end]].
* The ''Film/JamesBond'' movie ''Film/{{Spectre}}'' features the return of SPECTRE, the NebulousEvilOrganization from the early Bond films and later novels. The movie reveals [[spoiler:that SPECTRE was the true power behind, or was at least strongly connected to, QUANTUM, the organization whose agents served as the villains of the first two Craig-era movies, ''Film/{{Casino Royale 2006}}'' and ''Film/QuantumOfSolace'', as well as Raoul Silva from ''Film/{{Skyfall}}''. However, this trope only applies out-of-universe. The soft ContinuityReboot that occurred in ''Casino Royale'' means that this is the first time James Bond fights SPECTRE in this continuity.]]
* ''Film/ResidentEvilRetribution'' has [[spoiler:[[AIIsACrapshoot the Red Queen]], who was previously deactivated at the end of the first movie and was revived presumably between ''Film/ResidentEvilExtinction'' and ''Film/ResidentEvilAfterlife'']].
** ''Film/ResidentEvilTheFinalChapter'' has Wesker appearing as the main antagonist, [[spoiler:[[SummonBiggerFish until he calls on]] the original Dr. Issacs for help]].
* ''Film/{{Zoolander 2}}'' hints that Atoz, the new female fashion designer, is going to be the main villain. [[spoiler:Later on, Mugatu becomes freed from prison and is revealed to be the one assassinating the world's most beautiful people in order to kill all fashion designers and models, with Atoz actually being Katinka from the last movie in disguise.]]
* ''Film/FantasticBeastsAndWhereToFindThem'', despite being set in the same world as ''Literature/HarryPotter'', features Gelert Grindelwald as the GreaterScopeVillain for the franchise. The first film, however, depicts him as being a VillainOfAnotherStory, with his actions being present but only in Europe. Surprise — the villain isn't a follower, but Grindelwald himself.
* ''Film/SoloAStarWarsStory'' deals with Han Solo, Chewbacca, Lando, and several other smuggler allies having to do a heist job for Dryden Vos, the public leader of the Crimson Dawn crime syndicate. The inner workings of Crimson Dawn are left vague for most of the story (largely because they're too much of TheDreaded for anyone with half a brain to dig into that), but a climactic scene reveals that [[spoiler:the syndicate's true leader and the superior to Dryden Vos is none other than Darth Maul, the Sith Lord introduced in ''Film/ThePhantomMenace''.]]

* In ''Literature/ArtemisFowl: The Time Paradox'', the apparent villain-of-the-day (or yesterday) Damon Kronski turns out to be the pawn of [[spoiler:Opal Koboi]].
* ''Literature/ASeriesOfUnfortunateEvents'' plays with this:
** About half the books introduce a new character that turns out to be Count Olaf in disguise; however, the Baudelaires see through it early on and [[CassandraTruth spend the rest of the book trying to convince]] [[AdultsAreUseless the bumbling adults in charge.]]
** Also used for Olaf's many minions, at least one of whom always accompanies him in his schemes. Weirdly, the children never really are able to recognize ''them'' until the very end, despite the fact that the children are usually told that Olaf's minions just showed up in the area recently and they quickly notice suspicious characteristics about them. [[spoiler:For example, the Foreman with the bad wig turns out to be the Bald Man With The Big Nose, the doctor with the "unusually solid hands" turns out to be the Hook-Handed Man, and Officer Lucinda with her "lipsticked smile" turns out to be Esme Squalor]]. It's not until the end of the book that the identities are revealed, which leads to the siblings inevitably trusting the newly-captured Olaf into the hands of the kind, innocent doctor or police officer that they just met.
** In the last book, [[spoiler:there is Ishamel, a man the siblings never heard about from anyone on the vast V.F.D. organization (where everyone seems to know everyone) and was able to seemingly defeat both the Baudelaires and Olaf — and Kit Snicket. In the end, it also looked like he is the only one of the original people on the island to make it alive to the continent.]]
* In the first three books of ''Literature/TheBlackCompany'', Dominator is a well-known GreaterScopeVillain to Lady's BigBad, so when he [[spoiler:tries to hijack the plot in every book]], it's this trope in-universe. Subverted later in the series with new BigBad [[spoiler:well, BigBadWannabe]] Longshadow. It's heavily hinted he's someone the protagonists have faced before, supported by one of his minions turning out to be a previous antagonist and his own habit of going around in a mask and cloak that completely conceals his appearance. When they finally capture him, however, he turns out to be a complete stranger whose history is entirely unconnected to the previous books.
* ''Literature/BooksOfBayern'': In the fourth book, [[spoiler:Selia]] shows up again after having supposedly been executed at the end of the first book...and as if that wasn't enough, the same character claims to have been indirectly responsible for the events of books 2 and 3 as well.
* In ''The Crystal Prison'', the second book in the ''Literature/DeptfordMice'' trilogy, Nicodemus, the spirit controlling Madam Akkikuyu, turns out to be Jupiter, the evil god from the previous book.
* Substitute Ganon with Takhisis and you have the entire ''War of Souls'' trilogy in the ''Literature/{{Dragonlance}}'' series.
* ''Literature/HarryPotterAndTheChamberOfSecrets'' plays out like this. So a monster controlled by the Heir of Slytherin has been attacking students. At the end, we discover that [[spoiler:-surprise!- Voldemort]] was behind the entire thing.
* {{Subverted|Trope}} in ''Literature/HarryPotterAndThePrisonerOfAzkaban''. [[spoiler:Everyone said Sirius Black was a Death Eater, so an appearance of Voldemort was expected.]] It is the only book where Voldemort isn't the BigBad. [[spoiler:Although, the events in the climax of Book 3 lead to Voldemort's reincarnation in ''Literature/HarryPotterAndTheGobletOfFire'', so it's a sort of remote hijacking.]] A similar subversion happens in ''Literature/HarryPotterAndTheHalfBloodPrince'', where it seems like the "prince" might be Voldemort (a half-blood) but it turns out to be [[spoiler:Snape. He seemingly betrays and murders Dumbledore on Voldemort's orders, but is later revealed to have been a double-agent who was on the right side all along]].
* ''Literature/HonorHarrington'': The genetic-slavers (and DesignerBabies) of Mesa and [[EvilInc Manpower Inc.]] have basically been [[TheChessmaster puppeteering]] [[TheGoodKingdom the Star Empire of Manticore]] and the Republic of Haven since near enough the beginning of the series. Their {{plan}}s are almost [[Franchise/StarWars Palpatine]]-esque in their intricacy.
* ''[[Literature/KittyNorville Kitty Takes a Holiday]]'' is an interesting example in that "Ganon" is a [[spoiler:non-personified antagonist. The opening chapters are about Kitty trying to keep Ben's new lycanthropy infection from [[DrivenToSuicide driving him to suicide]]. After the initial crisis is resolved, the resultant RescueRomance is a B-plot through the remainder of the book. Meanwhile, the A-plot eventually leads Kitty and Ben to TheManBehindTheMan. It turns out that neither party can beat the other, so the good guys have to KnowWhenToFoldEm. The stress of failure causes Ben to wolf out, and the climax of the novel is Kitty chasing Werewolf-Ben through the woods, trying to find him and calm him down.]]
* At least from the perspective of the majority of the world, this is what [[spoiler:Satan]] does to the {{Antichrist}} in the Literature/LeftBehind series.
* In-universe example -- the main threat for most of the ''Literature/MalazanBookOfTheFallen'' is [[WoobieDestroyerOfWorlds the Crippled God]], but in the last few books, his power is usurped [[spoiler:by the Forkrul Assail, a KnightTemplar race of AbusivePrecursors, who intend to use it to scour the world of humanity, which they see as unsalvageably corrupt]]. While [[spoiler:the Forkrul Assail]] hadn't previously appeared as villains in the books themselves, they were a threat from the world's prehistory, so many of the characters, particularly the immortals, see it as this trope.
* In ''Literature/TheVorGame'', the various plots and counterplots wind up being overshadowed by a Cetagandan plot to re-invade Barrayar.
* ''Literature/WarriorCats'': Sol is probably the only villain in the entire series that isn't somehow connected to Tigerstar. And it's still unclear if he actually was or not.
* The original novel of ''Literature/YouOnlyLiveTwice''. So James Bond needs to get his mojo back after Blofeld got away and murdered his wife out of spite last time. Well, through a complicated series of events, Japan tosses him a relatively easy one: Some loon named Doctor Shatterhand is running a poisonous garden and encouraging suicide. Investigating that should jump-start him out of his funk... dum-da-da-da! It's Blofeld again! And he's ''crazy!''
* In Creator/RykESpoor's trilogy ''Literature/TheBalancedSword'', the ultimate mastermind behind all the BigBad's actions is revealed to be the Wolf King, Virigar, the BigBad of the ''Literature/JasonWood'' stories.
* ''LightNovel/TheUnexploredSummonBloodSign'': While each volume has its own set of antagonists, [[spoiler:the White Queen]] will always be revealed to be behind it all. Justified: [[spoiler:she's the strongest being in the setting, so any scheme worth the name will involve her in some capacity. Meanwhile, the Queen is completely obsessed with [[TheHero Kyousuke]], so she goes along with any plan that will let her encounter him]].
* ''Literature/TsarGorokhsDetectiveAgency'': Most cases eventually lead back to the EvilOverlord [[OurLichesAreDifferent Koschei the Deathless]]. So much so that the detectives are genuinely surprised when that sometimes turns out to ''not'' be the case, [[spoiler:like in ''The Plot of the Black Mass'' (villain is a demon) and ''Bride Elimination'' (villain is an Austrian diplomat)]]. Apparently averted in ''Tsar Koschei's Black Sword'', where Koshei is seemingly killed by the new BigBad [[OurDragonsAreDifferent Zmey Gorynych]], [[spoiler:but then it turns out that Koschei was only FakingTheDead and was behind Zmey all along]].

[[folder:Live-Action TV]]
* ''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 [[spoiler: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 ''Series/{{Arrow}},'' as of Season Five, [[ComicBook/{{Deathstroke}} Slade Wilson]] is the only BigBad who has ''not'' turned out to be connected 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 [[spoiler: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).
* 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.''
** Done '''twice''' in "[[Recap/DoctorWhoS10E3FrontierInSpace Frontier in Space]]", in which the Ogrons are quickly revealed to be working for the Master (in Roger Delgado'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 "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 "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 the new series, 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 Season 7, the Great Intelligence being behind everything would count as this. Turns out the villains in the Christmas special and the Bells of Saint John were just TheDragon to him.
** In Season 8, it turns out that Missy [[spoiler:is short for "Mistress" -- she's the Master, come back [[JokerImmunity yet again]]]].
* And the ''Doctor Who'' spin-off ''Series/Class2016'' had a huge example at the end of its first season - [[spoiler:the Governors are an apocalyptic PathOfInspiration working for the Weeping Angels]].
* 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, [[spoiler: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 [[spoiler: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.
** And in the old days, Shocker's Great Leader turned out to be behind any number of evil organizations. At least now it takes an ''actual revival of Shocker'' for this kind of thing to happen; in the old days, it'd be Creator/GoroNaya popping up to say "[[Series/KamenRiderBlade Undead]]? [[Series/KamenRiderHibiki Makamou]]? [[Series/KamenRiderOOO Greeed]]? All my plan even if there's ''no freakin' way.''" at the end of a series that never seemed to have anything to do with him or those others.
** It seems ''Series/KamenRiderDouble'', ''[[Series/KamenRiderOOO OOO]]'', and ''[[Series/KamenRiderFourze Fourze]]'' are getting hijacked by Foundation X.
* 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, [[spoiler: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'', [[spoiler: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}}'', [[spoiler: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.]]
* At the end of season 4A of ''Series/OnceUponATime'', after the SnowQueen [[spoiler: [[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 [[BigBadDuumvirate with various other previously seen and new villains along the way]].
* 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 ([[spoiler:likely due to his being dead]]), but he does [[spoiler: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' archnemesis 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.
* ''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 succesfully [[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'':
** More obvious was in the ''Series/StarTrekTheNextGeneration'' episode "Descent", when the rogue Borg the ''Enterprise'' has been chasing turned out to be led by [[EvilTwin Lore]].
** In ''Series/StarTrekDeepSpaceNine'', the revelation that the Breen were working for the Dominion was done in a similar fashion. And that the Orion Syndicate had been working with the Dominion too, in an earlier episode.
* The conclusion of ''Series/TinMan'' reveals that the BigBad [[GodSaveUsFromTheQueen Princess Azkadellia]] is actually a descendent of [[Literature/TheWonderfulWizardOfOz Dorothy Gale]], who 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 [[spoiler: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. [[spoiler:Once the final monster is destroyed, the unknown hand reveals himself to be an entire evil Ultra known as "Dark Zagi".]]
* ''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'', [[spoiler: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, [[spoiler:Max, the man behind Season 2's events, is the BigBad]].
** Subverted in season six; [[spoiler:it seems like the Chinese are pulling this, but Phillip Bauer turns out to be the actual antagonist]].
** In the ''Live Another Day'' miniseries, [[spoiler: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]].
* The miniseries of ''Series/TheXFiles'' seems to have [[spoiler:the Cigarette Smoking Man returning BackFromTheDead and as the BigBad once again]].
* 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. [[spoiler:However, someone is actually replicating Scratch's M.O. down to the letter to make it appear to be him, who 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, who 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, 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.]]

[[folder:Myths & Religion]]
* Throughout Literature/TheBible, everyone who commits an act of sin can be said to be tempted by Satan, directly or otherwise. However, the Book of James doesn't buy blaming Satan (or God, for that matter) as a FreudianExcuse:
--> When tempted, no one should say, “God is tempting me.” For God cannot be tempted by evil, nor does he tempt anyone; but each person is tempted when they are dragged away by their own evil desire and enticed.
* In Myth/NorseMythology, this gets combined ''with'' HijackedByJesus; after the Christianization of Norse Mythology, many stories had Loki written to be a more typical villain rather than the [[FallenHero Fallen]] GuileHero he previously was, leading to one notable example with Baldir's death. Everything in creation (even the flora) have to shed tears to bring the God Baldr back to life, but there is one Frost Giantess who refuses, and as a result, he can't. The Frost Giantess turns out to be Loki, who killed Baldr in the first place, in disguise, both points of which didn't come in until later versions.

[[folder:Pro Wrestling]]
* In Wrestling/{{WCW}}, there was the infamous Wrestling/{{Sting}} vs. the Black Scorpion angle. In August 1990, after wrapping up another chapter in his on-again/off-again feud with Wrestling/RicFlair, Sting started being harassed by a mysterious masked man who spoke with a heavily altered voice. The standard "masked wrestler" plotline quickly got out of control, incorporating bizarre promos, "messengers" that attacked Sting at house shows, and ringside stage illusions. After four months of this nonsense, the Black Scorpion was finally revealed to be... Ric Flair. Behind the scenes, this was an AuthorsSavingThrow -- WCW constantly alluded to the Black Scorpion actually being [[Wrestling/UltimateWarrior the Ultimate Warrior]] in an attempt to get Warrior to jump ship from WWF[[note]]Sting and UW started their careers together in California before going to Memphis as the Freedom Fighters and then to "Cowboy" Bill Watts' Mid-South/UWF as the Blade Runners, Flash and Rock, before going their separate ways.[[/note]] When it didn't work, they shoehorned Flair in instead.
* In early 1993 Wrestling/{{WWE}}, manager Wrestling/HarveyWippleman was not happy about how Wrestling/TheUndertaker had defeated Wippleman's man Wrestling/{{Kamala}} in the Casket Match at ''Wrestling/SurvivorSeries 92'', leading to Kamala's [[HeelFaceTurn face turn]] and siding with Reverend Slick. On the January 16, 1993 (taped December 14, 1992) episode of ''WWF Superstars'', Wippleman announced that the [=WWF=] would never be the same after he dropped "the big bomb." At the ''Wrestling/RoyalRumble,'' January 24, 1993, Wippleman revealed what "the big bomb" was: the 7'7" (billed as 8'0"), 400 lbs.+ the Giant [=Gonzales=] (real name Jorge Gonzales, formerly Wrestling/{{WCW}} [[{{Face}} babyface]] El Gigante), who interfered in the match and eliminated the Undertaker! May he rest in peace.
* Another WWE mystery: "Who ran over [[Wrestling/StoneColdSteveAustin "Stone Cold" Steve Austin]]?" Well, the man driving the car was revealed to be Wrestling/{{Rikishi}}, whose lame MotiveRant killed any potential heat. Rikishi was so ill-fit for the {{Heel}} role that after one month the much better established Wrestling/TripleH was revealed to be TheManBehindTheMan. In reality, the mastermind couldn't have been anyone BUT Triple H. Triple H assaults Austin backstage, runs off, lures Austin out into the parking lot, where Rikishi just randomly happens to be in a car in the parking lot ready to run him over. Despite Triple H's insistence right before Rikishi's reveal that he was planning to lead to Austin to a beatdown, the variables are just too unlikely for it to be anybody but Triple H.
* In 1999, ''Wrestling/{{WWE}}'' featured a long and convoluted storyline about Wrestling/TheUndertaker and his Wrestling/MinistryOfDarkness attempting to seize control of WWE from Wrestling/{{Vince McMahon}} under the orders of a mysterious figure known only as "The Higher Power". This "Higher Power" turned out to be... [=Vince McMahon=]. The Ministry Of Darkness then merged with Wrestling/TheCorporation to become the Corporate Ministry, and about five months of storyline were thrown out the window. To be fair, this wasn't the original plan - [[spoiler:Mick Foley]] was originally planned as the higher power, but he turned down the angle because he felt he was too physically broken down to do the angle justice. Going with Vince was Plan B.
* Wrestling/MollyHolly tried to hijack [[Wrestling/LisaMarieVaron Victoria]] by giving her further training and direction, but it didn't work, as she really couldn't control Victoria at all. She later did gain the servitude of Wrestling/GailKim by threatening to beat Gail up until she got it.
* In Wrestling/{{TNA}}, [[Wrestling/JamesMitchell "Father" James Mitchell]] took the Gathering (CM Punk and Julio Dinero) away from Wrestling/{{Raven}}, who had originally {{brainwashed}} them.
* In 2003 WWE, Sean O'Haire was starting a [[TheCorrupter Corrupter]][=/=]Devil's Advocate gimmick, where he would tell people to do unusual or outrageous things, topping it off with his CatchPhrase, "I'm not telling you anything that you don't already know." On the February 6th ''[=SmackDown!=]'' he convinced [[Wrestling/LondonAndKendrick Brian Kendrick]] to streak after A-Train {{Squash|Match}}ed Shannon Moore. On the March 13th show, he convinced Dawn Marie, a {{Heel}} herself, to "flash" the crowd[[note]]This was the same night that Wrestling/TorrieWilson, Wrestling/StacyKeibler, and Nidia all appeared on the ''Girls Gone Wild'' [=PPV=], though none of them actually got naked. Dawn had tape over her breasts and the rope was in the way.[[/note]] Then [[Wrestling/RoddyPiper "Rowdy" Roddy Piper]] returned to WWE during the Wrestling/HulkHogan vs. Vince [=McMahon=] match at ''Wrestling/{{WrestleMania}} XIX'' on March 30th as a heel, attacking both guys. O'Haire got turned into Piper's lackey as part of the whole ridiculous feud with Hogan[=/=][[Wrestling/StephanieMcMahon Stephanie [=McMahon=]]][=/=][[Characters/WWERuthlessAggression Zach Gowen]] vs. Vince[=/=]Piper[=/=]Wrestling/{{Sable}}[=/=]O'Haire[=/=]A-Train[=/=]Wrestling/TheBigShow and maybe some other people. Even after Piper was fired in June, O'Haire never really got any kind of chance to revisit the gimmick and left in 2004.
* Wrestling/{{Christian}} did this to WWECW upon his 2009 return. In fact, one could argue that he and [[Wrestling/TheWorldsGreatestTagTeam Shelton Benjamin]] were the only reason anyone would watch the show by that point.
* Wrestling/TheNexus was a group of scorned rookies out for revenge against the mainframe of the WWE... only for them to eventually become lackeys of the already well-established Wrestling/CMPunk, one of the original NXT mentors, after he disposed of their initial leader, Wrestling/WadeBarrett. Barrett would form the Corre in an attempt at revenge.
* By 2012, the Canadian Ninjas had been campaigning on and off against Wrestling/CheerleaderMelissa for two years. After their attack on Wrestling/{{SHIMMER}} Volume 45, it was revealed they were after a bounty put on Melissa by Sweet Saraya, an opponent she hadn't faced in ''five years''.
* In Ohio Valley Wrestling, it was originally assumed Kevin Thorn had turned Shelly Martinez into the {{wrestling|monster}} vampire Ariel but in the lead up to Wrestling/{{N|ationalWrestlingAlliance}}WA Vendetta Pro's 2013 ''Immortal Fear'' event, it was revealed she was instead turned by and still loyal to the much longer established Billy Blade.
* When [[Wrestling/{{FMW}} Frontier Martial-Arts Wrestling]] was revived in 2015, one of the first things the returning FMW Seikigun had to deal with was NOSAWA's new Monster-gun faction, which would quickly be converted into the W*ING Monster-gun by long established FMW figure W*ING Kanemura.

* In the AudioPlay/BigFinishDoctorWho story "[[Recap/BigFinishDoctorWho030SeasonsOfFear Seasons of Fear]]" it turns out that Sebastian Grayle's masters are the Nimon.
* Parodied in an EasterEgg on the old ''Radio/AdventuresInOdyssey'' website where, among other tomfoolery, arch-villain Dr. Blackgaard turns out to be the mastermind behind the Novacom Saga... with a possible reference to the fact that there ''were'' plans for Mayor Margaret Fey to be the ultimate villain. Somehow.

[[folder:Tabletop Games]]
* After the release of Infernals in the second edition of ''TabletopGame/{{Exalted}}'', the Ebon Dragon seemed to have his hand in everything. He created the Unconquered Sun (Okay, that had been there since early first edition). He made contact with the Neverborn for the purposes of creating the Infernal AND Abyssal Exalted. He abducted the Scarlet Empress. He contacted the Viator of Nullspace and set him on his current quest to remake the Great Maker. Certain lines in Return of the Scarlet Empress -- the storyline in which one has at least four other Yozis to worry about, along with their own forces and those with the Realm, and he still manages to arise as the clear dominant villain of the entire game -- even strongly suggest he was behind the Great Curse.
* TabletopGame/LegendOfTheFiveRings Gold Edition story arc introduced Daigotsu, the mysterious new lord of the Shadowlands. Daigotsu was able to dispatch the venerable powerhouse characters Toturi and Kyoso no Oni with ease and brought with him never-before-seen monsters such as the Tsuno and Onisu. He even managed to level Rokugan's capital city of Otosan Uchi... at which point he released [[GodOfEvil Fu Leng]], the setting's de facto BigBad from the realm of the dead and who then took on the role of the arc's FinalBoss. Interestingly, Daigotsu played an indirect role in Fu Leng's defeat thanks to [[MagnificentBastard Hantei Naseru]] running a successful BatmanGambit on the latter regarding the former's loyalty.

* Makuta from ''Toys/{{Bionicle}}'' got into the habit of this. After the Bohrok arc, it was revealed that he released them in the first place to buy time to recover from his prior defeat. In Metru Nui, he was the mysterious mastermind behind everything. And then when a group of thugs called the Piraka went after a treasure called the Mask of Life, we eventually found that Makuta manipulated them into doing so. Most of the other arcs, though, stated up front that Makuta was at least in charge of the other villains even if he didn't appear personally (with two exceptions - he was unaffiliated with the Barraki, and even quietly supported the heroes against them for his own reasons; and in the first arc on Bara Magna he just plain wasn't involved).

[[folder:Video Games]]
%%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)
* Several times in ''Franchise/TheLegendOfZelda'' series, the hot new BigBad turns out to simply be a pawn of Ganon or is [[SealedEvilInACan trying to revive him]]. Notably, most of these games also feature the Master Sword. Surely the nature of these examples and the Trope Namer should invalidate the need for spoilers. It's pretty obvious at this point.
** ''[[VideoGame/TheLegendOfZeldaALinkToThePast A Link to the Past]]'' features an odd, ambiguous situation as main villain Agahnim is said, depending on 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, furthered by Agahnim's {{Leitmotif}} becoming Ganondorf's theme from ''Ocarina of Time'' onward, Ganon hijacked the game from ''himself''.
** In the ''[[VideoGame/TheLegendOfZeldaOracleGames Oracle]]'' games, [[spoiler:the Twinrova sisters, Kotake and Koume, are the real {{Big Bad}}s. Ganon is the FinalBoss, but he does not directly have a hand in the plot, making him more of a GreaterScopeVillain]]. [[spoiler:Twinrova]] is also pulling a Hijacked by Ganon at the same time: ''Oracle of Ages'' and ''Seasons'' depict Veran and Onox as the main antagonist respectively, only revealing [[spoiler:Twinrova]]'s involvement near the end of the first game you play.
** ''[[VideoGame/TheLegendOfZeldaFourSwordsAdventures Four Swords Adventures]]'' is a odd mixture of this and TheManBehindTheMan. Vaati is a recurring villain from the [[VideoGame/TheLegendOfZeldaFourSwords prequel game]], and is further established in [[VideoGame/TheLegendOfZeldaTheMinishCap an earlier prequel]], 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 was already an established villain as an alternate to Ganon, so Ganon becomes TheManBehindTheMan as well.
** Then there is Zant of ''[[VideoGame/TheLegendOfZeldaTwilightPrincess Twilight Princess]]'', who, after being built up as "The Twilight King," becomes the victim of yet another twist hijack by Ganon. While this caused a lot of debate among fans during the first few years following the game's release, it was already known before the game came out that Ganon was going to be in the plot; and Zant ''does'' allude to Ganondorf being behind him the ''first time Link and Midna encounter him'' (completion of the third dungeon).
** Played with in ''[[VideoGame/TheLegendOfZeldaSkywardSword Skyward Sword]]'', 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''), [[spoiler:the ending reveals that the spirit of Ganon that keeps pursuing Zelda and Link's descendants is [[HereditaryCurse the incarnation]] of [[ThePowerOfHate the hatred]] of Demise. Effectively, every single hijacking Ganon ended up being hijacked by Demise ultimately.]]
** Zig-zagged in ''VideoGame/TheLegendOfZeldaALinkBetweenWorlds''. [[spoiler: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. However, he actually [[TheStarscream betrays Hilda]], turns her into a painting and absorbs ''her'' power, once again keeping his position. Hijacked by [[FanNickname Yuganon]], indeed. There's also the implication that Yuga is the [[AlternateUniverse Lorule]] counterpart of Ganon, meaning that Hilda got hijacked by ''two Ganons at once''.]]
** Zig-zagged [[spoiler:but ultimately played straight]] in ''VideoGame/HyruleWarriors''. 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, [[spoiler: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 she's dealt with. In an amusing twist from the usual, [[VillainShoes the game lets you ''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."
* Played as an InternalReveal in ''VideoGame/AceCombat5TheUnsungWar'': the masterminds behind the war between Osea and Yuktobania turn out to be the same [[spoiler: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.
* In the ''VideoGame/BatmanArkhamSeries'', ComicBook/TheJoker is always the real BigBad.
** In ''Asylum'', it's fairly straightforward; Joker engineered the prison break at the titular Asylum.
** In ''City'', while trailers did feature the ensemble, it seemed that Hugo Strange and TYGER would be much more the overarching threat, [[spoiler: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 ''Origins'', trailers hyped up Black Mask, a relatively unknown villain to non-comic fans, as the BigBad who hired eight assassins to kill Batman. [[spoiler: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, ''Knight'' follows suit -- Scarecrow and the Arkham Knight are the BigBadDuumvirate, but the Joker's the GreaterScopeVillain. [[spoiler: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 ''Origins''' "Cold, Cold Heart" DLC.
* ''VideoGame/BionicCommando'' for the NES sets up [[TheGeneralissimo Generalissimo Killt]] as the villain of the story due to his attempts to build an "[[ThoseWackyNazis Imperial Army]]" LostSuperweapon known as "The Albatross," an [[StupidJetpackHitler airborne warship covered in flamethrowers]]. At the last second, Killt is killed off by a revived "Master D," described as a villain who had appeared earlier in the series and the one responsible for the creation of the Albatross. He launches the Albatross and attempts to take over the world. Master D is so obviously UsefulNotes/AdolfHitler that the pretense otherwise is beyond clingfilm thin (and not even bothered with in the original Japanese, where they just admitted it was a revived Hitler). The game itself notes that they had defeated the Imperials and Master D before and implies that the game depicting these events was ''VideoGame/{{Commando}}'' starring Super Joe, but no such boss appears in the top-down game that would correlate to Master D. The ''Bionic Commando'' arcade game, on the other hand, has a General final boss with officers in gray SS uniforms, so it's possible that this is the previous battle with Master D that the NES ''Bionic Commando'' refers to (even though the General and Master D look nothing alike). The Japanese version throws all this out the window and causes Killt to be meta-Hijacked by Ganon instead, with the real life fascist dictator Hitler serving as the true threat instead of the tinpot dictator Killt.
* Franchise/{{Blazblue}}: The series 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 the second game along with his partner-in-crime [[MadScientist Relius Clover]], but they're both ultimately pushed aside 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 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.
* 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; [[spoiler: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. [[spoiler: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 [[spoiler:a TomatoInTheMirror -- you can't expect to ''fight'' Dracula if you're ''playing'' him, right?]]
** ''[[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. As a wraith, but still.
** ''VideoGame/{{Castlevania 64}}'': [[spoiler:You know that kid Malus? The one who claims he was kidnapped by Dracula's followers along with the other children? ''That's'' Dracula. That vampire you fought earlier in the game was a faker.]]
** In both ''[[VideoGame/CastlevaniaCurseOfDarkness Curse of Darkness]]'' and ''[[VideoGame/CastlevaniaOrderOfEcclesia Order of Ecclesia]]'', Dracula yet again comes out of nowhere at endgame. [[spoiler: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, [[spoiler: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]]'': [[spoiler: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'', [[MemeticMutation it's all a Nemesis plot]]; he 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: [[spoiler:the Nictus, including Requiem and the 5th Column]].
** The [[AncientRome Cimerora]] zone was only introduced after the appearance of [[TimePolice Ouroboros]] [[spoiler:whose chief has a SignificantAnagram]].
** True veterans of the game know it's only a matter of the time until the writers make Nemesis responsible for [[spoiler: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 [[spoiler:Malta]] pulling the strings.
* ''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.
* Often in ''Franchise/DanganRonpa'' with [[spoiler:Junko Enoshima]], which is impressive considering [[spoiler:she died in the first game]].
** In ''VisualNovel/SuperDanganRonpa2'', [[spoiler:a Junko AI hijacked the Neo World Program and inserted Monokuma]].
** In ''LightNovel/DanganRonpaZero'', [[spoiler:Junko temporarily wiped her own memory to become the protagonist]].
** In ''VideoGame/AbsoluteDespairGirls'', [[spoiler:Junko AIs were controlling Shirokuma and Kurokuma, meaning she hijacked ''both sides'' of the conflict]].
** Subverted in ''Anime/Danganronpa3'''s Future Arc, [[spoiler:where Junko has nothing to do with the Final Killing Game]]. Played straight in the Despair Arc [[spoiler:where she literally hijacks the plot midway and it is shown how she plunged the world into despair.]]
** PlayedWith in ''VisualNovel/NewDanganRonpaV3'', in which the mastermind, upon being cornered, discusses this trope to deflect the blame, before [[spoiler:she cosplays as her... but still has nothing to do with Junko at all. In addition, when Kokichi Oma was thought to be the mastermind, the true mastermind makes everybody believe that Kokichi is a Remnant of Despair. In actuality, Kokichi has no idea who Junko Enoshima even was.]]
* In ''VideoGame/DawnOfWar II 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 assult on the sub-sector Aurelia was orchestrated by [[spoiler:the daemon, inadvertently released by Gabriel back in the end of the first game]].
* 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 [[spoiler:JC Denton, the player character from the original ''VideoGame/DeusEx'']].
* 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 Lucian. But Lucian was never an antagonistic figure before... and within the FinalBoss fight with Dallis and Lucian, ''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.
* 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.
* ''VideoGame/FiveNightsAtFreddys2'' introduces newer "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 (the new Foxy) stop attacking almost entirely until the bonus nights.
* 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, [[spoiler: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 ''that'' character to have been dead since [[VideoGame/GoldenSun the first two games]], so it's a shock to ''them'' when his identity is revealed. He laughs. [[spoiler: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 [[spoiler:until TheStinger]], and the roc feather quest takes a backseat to stopping the Grave Eclipse.
* In ''VideoGame/Jak3Wastelander'', it's revealed that [[spoiler:[[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 [[spoiler: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 ''coded''. The rest of the time:
** 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.
** ''Chain of Memories'' introduced Organization XIII, which served as the villains of that game and ''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 ''358/Days'' spin-off that takes place in the same timeframe.[[note]]Technically the Organization members in ''Chains'' 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 ''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.
** ''Dream Drop Distance'' had Ansem and Xemnas return with a new villain, which turned out to be a younger Master Xehanort travelling 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.
* While not present in the main story, 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, [[spoiler: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 [[spoiler:sacrifices himself and his minions to revive his Dark Lord Void Termina - who is later revealed as a reincarnation of the [[VideoGame/KirbysDreamLand3 Dark Matter race]].]]
* 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. [[spoiler: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.]]
* ''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 [[spoiler:Jack's past in the games]]. Then, get ready for this, [[spoiler:'''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 pretty much shrugged and said "It's probably Reapers" in the first conversation about the Collectors.
* This is the trademark tactic for Dr. Wily and Sigma in the ''Franchise/MegaMan'' series.
** He pretended to reform in ''VideoGame/MegaMan3'', and in all subsequent main series games except ''VideoGame/MegaMan7'' and ''VideoGame/MegaMan8'', he turns out to be using the initial villain or some other phenomenon as a decoy. The reason he doesn't in ''7'' is that the game begins with Wily being arrested, but his robots activate themselves and free him. Also does it in ''VideoGame/MegaManV'' for the Game Boy with the Star Droids [[spoiler:though in a bit of a twist, he is ''not'' the final boss of this 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 named "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'' onwards, to the point it's a twist that he ''isn't'' the BigBad of ''VideoGame/MegaManX8''. It gets {{lampshade|Hanging}}d in ''VideoGame/MegaManX4'' when Split Mushroom responds to a demand to reveal the mastermind behind the game's plot with his [[MemeticMutation meme-tastic]] CatchPhrase "Take a wild guess", after which his lifebar appears, blatantly carrying [[GratuitousGreek Sigma's]] [[BroughtToYouByTheLetterS logo]], 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'', when the BigBad was ''not'' Sigma, it was Gate, and Gate resurrected Sigma to use him to destroy X, but Sigma CameBackWrong and was obviously not the controlling force behind the plot.
** ''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. There's also fan theories that Serges and Isoc, each originating from different games in the ''X'' series, are either Dr. Wily somehow, or that like Sigma, Wily's consciousness endures and finds host bodies to act through.
** 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 third and fourth games, uses a robot ([[spoiler:Zero's original body, specifically]]) that Wily built.
** Finally, the ''VideoGame/MegaManZX'' series that continues the ''Zero'' series, the original Biometal W is a part of the Ragnarok space station from ''Zero 4'' and has Weil's consciousness possessing it due to his FusionDance with it at the climax of the game to try and kill Zero only for Zero to destroy him and the station, 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.
** In the ''VideoGame/MegaManBattleNetwork'' games (which are an AlternateUniverse from the rest of the series), Wily hijacks ''2'' when the main villain of that game reveals in the third he was working under orders from Wily. ''4'' and ''5'' do ''not'' have him, [[spoiler:making it actually effective when he appears in ''6'' and reveals his EvilPlan]]. However, the villain of ''4'' and ''5'' is the organization Nebula, led by Wily's son.
* A complicated quadruple example in the Metal Gear 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 ''VideoGame/MetalGearSolid'', and goes rogue. Then in ''VideoGame/MetalGearSolid4GunsOfThePatriots'', Liquid seizes control of the SOP system from The Patriots, becoming the BigBad. [[spoiler: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.
* ''Franchise/{{Metroid}}'':
** In ''VideoGame/MetroidOtherM'', the events aboard the Bottle Ship are the fault of [[spoiler:MB, who is essentially a resurrected Mother Brain]]. The postgame is a more jarring and unexpected example. [[spoiler: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/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, [[spoiler: 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/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 [[spoiler:Kabuto]] for unknown reasons (it's unclear whether he did it on his own, or for [[spoiler: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/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, [[spoiler: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 OneHundredEight 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 [[spoiler: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 ''other'' evil teams (taken from parallel dimensions) as high-ranked members.
* ''Franchise/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 [[spoiler: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 subverts this; they have nothing to do with the plot, simply serving as {{Easter Egg}}s to observant players.
* ''Franchise/SonicTheHedgehog'':
** [[spoiler:Dr. Eggman and Eggman Nega]] in ''VideoGame/{{Sonic Rush|Series}} Adventure''.
** In an unusual example of one previously-established villain hijacking ''another'', the "Eggman" faced in ''VideoGame/SonicHeroes'' turns out to actually be a disguised Metal Sonic.
** ''Both'' Classic and Modern Dr. Eggman in ''VideoGame/SonicGenerations''.
** ''VideoGame/SonicLostWorld'' has Sonic and Eggman team up for an EnemyMine early in the game, Eggman looking upstaged by the game's villains for the bulk of the game, [[spoiler:but at the start of the last area, Eggman fakes his death and sneaks off to complete his final mech in time to be the game's 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 [[spoiler:as a ridiculously hot woman]]. Talk about having it in for your son...
* [[spoiler:Andross]] also pulled this one in ''VideoGame/StarFoxAdventures''. [[spoiler:You even have to beat him the same way as in ''64''.]]
* In ''VideoGame/StarTrekOnline'', it's revealed that, ultimately, the real BigBad was [[spoiler:the Iconians, whom ''Series/StarTrekTheNextGeneration'' established as being long extinct. Not only are they not, they are also behind most, if not all, of the big conflicts going back to, at least, the Dominion War.]]
* ''Franchise/SuperMarioBros''
** Bowser in ''VideoGame/SuperMarioSunshine''. It turns out he's the father of Shadow Mario, a.k.a. Bowser Jr.
** 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.
** Played with in ''VideoGame/MarioAndLuigiDreamTeam'', the supposed BigBad, Antasma, forms an [[BigBadDuumvirate alliance]] with Bowser, but from the first minute is pretty clearly planning to backstab Bowser and Hijack the game. Suddenly it turns out Bowser saw this too and hijacked Antasma ''first.''
** ''VideoGame/LuigisMansion'' subverts this. The final boss, King Boo, only fights in a Bowser costume, so 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'' plays 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 Mega-Bug that was a constant yet ignored presence throughout the entire game.
* Although Master Hand is the flagship FinalBoss in the ''VideoGame/SuperSmashBros'' series, it subverts this trope in VideoGame/TheSubspaceEmissary. 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 [[GambitPileup yet another villain was controlling Master Hand the whole time]].
* In ''VideoGame/SystemShock 2'', you initially believe that The Many is the BigBad, having hijacked the Von Braun's crew with mind control. [[spoiler: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.]]
* ''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, ''[[VideoGame/RatchetAndClankFutureQuestForBooty 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 [[spoiler: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.]]
* Averted in ''VideoGame/ResidentEvil7Biohazard''. [[spoiler: The Umbrella Corporation doesn't have anything to do with this incident at all, and in fact seemed to have joined up with the B.S.A.A. in the intervening years between ''6'' and ''7''.]]
* ''VideoGame/Splatoon2'', literally from the moment you open the box, starts building up Callie, having undergone a FaceHeelTurn, as the BigBad of the single-player campaign. Once you open up the final Boss Kettle, though... [[spoiler:Nope! Callie is BrainwashedAndCrazy, and the ''real'' villain is DJ Octavio, just like last time.]]
* ''VideoGame/SuperRobotWars'':
** [[Characters/SuperRobotWarsAlpha Euzeth Gozzo]]. In ''VideoGame/SuperRobotWarsAlpha'', the player is led to believe [[Characters/SuperRobotWarsAlpha Laodecia Judecca Gozzo]] and [[spoiler:[[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. [[spoiler: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 [[spoiler:[[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]]''. [[CrowningMusicOfAwesome Cue]] ''[[https://www.youtube.com/watch?v=58gIsVJ7NuQ Beyond the Time]]''.
* 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, [[spoiler:The Marquis suffers DeathByIrony, and [=LeChuck=] reveals that his "good" act was just that, an act, and ''kills Guybrush'']].
* 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 [[spoiler: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 ''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 AI rabbit named Zero III. [[spoiler:As it turns out, both Zero III and his creator are working with the original Zero. 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 ''VideoGame/Wasteland2'' the TrueFinalBoss is [[spoiler: [[AIIsACrapshoot the Base Cochise AI]], the BigBad from [[VideoGame/{{Wasteland}} the first game]] that [[RobotMaster Matthias]] was trying to resurrect and [[EvilIsNotAToy ended up getting controlled by]].]]
* The TrueFinalBoss of ''VideoGame/WorldOfWarcraft'''s ''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.
** Kil'jaeden and Archimonde were also behind most of the events of the [[RealTimeStrategy RTS]] ''VideoGame/{{Warcraft}}'' games. Horde invasion? That was them. The Scourge? Yep. Illidan? Kil'jaeden again. Though that is more due to them being the GreaterScopeVillain.
** 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.
** The Burning Legion does have local competition in the form of the [[EldritchAbomination Old Gods]], who control two of the four elemental lords, the Qiraji, living Nerubians, the Watchers of Ulduar, the Twilight's Hammer cult, ''[[ExpansionPack Cataclysm]]'''s BigBad Deathwing, and yet-to-be-seen Queen Azshara. This is subverted in the ''Mists of Pandaria'' expansion. Garrosh manages to steal some power from a dead Old God, but apparently his ever-increasing aggression and megalomania were not influenced by them. He was just a {{Jerkass}}.
** Even the Burning Legion invasions of Azeroth are mere pawns to the Old Gods. It was the Old Gods who (probably) originally corrupted the Highborne into opening the portal through which the Burning Legion first learned of Azeroth. Why? So their other pawn, Netharian, would have a reason to craft the Dragon Soul, which they could corrupt and use to destabilize the portal giving them a means to break free from their prisons. Everything since has been an adaptation to their plans after each setback. They play the long game, and we haven't seen the end of it.
* On ''[[VideoGame/AeroTheAcroBat Zero the Kamikaze Squirrel]]'', the mastermind behind Jaques Le Sheets' scheme is [[spoiler:Edgar Ektor]].
* ''VideoGame/Injustice2'': So after the first ''VideoGame/InjusticeGodsAmongUs'' ends 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'' thought 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 at will]]? Yeah... '''[[{{Determinator}} no]]'''.

[[folder:Web Comics]]
* In ''Webcomic/{{Adventurers}}'', Khrima was the first villain, only to later be hijacked by Eternion. This is parodied, like everything else in ''Adventurers!'', when Khrima and Eternion have an election campaign on who gets to be the FinalBoss. Eternion got his boss fight, but Khrima afterward comes from out of ''nowhere'' with a VeryDefinitelyFinalDungeon and the FinalBoss fight.
* The "Army Of One" storyline in ''[[WebComic/TheAdventuresOfDrMcNinja Dr McNinja]]'', where the antagonist(s) seem to be a bunch of sky pirates who have kidnapped a clone of Doc, but the whole thing is really a plot by [[spoiler:Frans "I was pretty sure you were dead" Rayner, the main villain of the D.A.R.E. plotline from years ago.]]
* In ''Webcomic/SluggyFreelance'', [[spoiler:the "wraiths" attacking the [[AnotherDimension other dimension]] in the "[[http://beta.sluggy.com/daily.php?date=070205 Aylee]]" arc are actually members of Aylee's species, who, not counting Aylee's evil clone, hadn't appeared since Aylee was introduced 10 years previously]].
** Not to mention several dangerous situations set up by [[spoiler:demons who appear to be fragments of K'Z'K', the demonic BigBad from several early arcs]].
** And then there's [=HeretiCorp=], which at least usually has its logo on everything, except during its man-behind-the-man-who-was-actually-behind-the-first-man-anyway plots. Really, it's getting less "Is this _____ or a new enemy?" and more "Is this ____ or ____?"

[[folder:Web Original]]
* In ''WebAnimation/ArbyNTheChief'', [[spoiler:Chaos Theosis, the main antagonists of Season 6, were actually working for Trent Donnovich, who was the main antagonist of Season 5.]]
* In ''WebAnimation/ChaosFighters II''-Chemical Siege, after the true villain is revealed as [[spoiler:Etphan Signis]], when Enrei and Gareia finished him, it was revealed that [[spoiler:Thanic Snader]], the BigBad of ''Cyberion Strike'', did everything, including [[spoiler:mind-controlling Etphan so that he can leave Etphan doing the dirty work]].
* In ''WebAnimation/{{Ducktalez}} 7'', The Beagle Boys were run by [[spoiler:Julia Roberts, who was reconstructed by Eric Roberts after the sun nearly killed Julia in 3]].
* At the conclusion of ''Blog/{{Moonstuck}}'', [[spoiler:the "Nightmare Woona" who has caused most of the trouble is revealed to actually be Discord.]]
* In ''WebVideo/ThereWillBeBrawl'', we do end up getting a non-Zelda example for the TropeNamer, Ganondorf. [[spoiler:Then given another example in-universe when ''he'' is hijacked by ''[[SerialKiller Kirby]]'', who had been a problem to the kingdoms in the past.]]
* 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 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.]]
** {{Downplayed}} in Book 3 of the SequelSeries, ''WesternAnimation/TheLegendOfKorra'': [[spoiler:It's revealed in "The Stakeout" that Zaheer and his gang are part of a group called the Red Lotus, which [[EvilUncle Unalaq]] (TheDragon in Book 2) was initially part of.]]
* Season 3 of ''WesternAnimation/Ben10'' introduced in one episode an 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 Knight 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 in-universe example; in the first episodes, it seems like [[EgomaniacHunter Khyber the Huntsman]] is the BigBad. However, it's eventually revealed he actually is working for [[TheManBehindTheMan 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, [[spoiler:resurrecting Shendu in order to obtain the wayward [[PlayingWithFire Dragon Talisman]] power]]. [[EvilIsNotAToy The results are obvious.]]
* In ''[[WesternAnimation/JusticeLeague Justice League Unlimited]]''
** It's revealed that [[spoiler: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, [[spoiler: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 an BlackAndWhiteMorality villain take over [[InvokedTrope so they could have a proper fight finale]].
** In the subsequent story arc, this happens ''twice''. [[spoiler: 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 Darksied instead]].
* ''WesternAnimation/MyLittlePonyFriendshipIsMagic'': {{Double Subver|sion}}ted. When vines from the Everfree Forest started invading Ponyville and the princesses went missing in the episode "[[WesternAnimation/MyLittlePonyFriendshipIsMagicS4E1PrincessTwilightSparklePart1 Princess Twilight Sparkle]]", everyone assumed it was a new threat or villain causing all this. In [[WesternAnimation/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 [[spoiler:seeds that the recently reformed villain [[MadGod Discord]] planted right before his defeat by Celestia and Luna over a millennium before. The Tree of Harmony's power managed to keep them from growing for that long.]]
* ''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.
* In ''Tintin and the Lake of Sharks'' (1972) based on an original story, Tintin and friends faces a criminal organization specializing in making art forgeries lead by the mysterious "Shark King". It turns out "Shark King" is [[spoiler: Roberto Rastapopoulos, Tintin's most recurring villain.]]
* In second season of ''WesternAnimation/{{WITCH}}'' first season's BigBad, Phobos, escapes in one episode and takes over team of recurring vilains, Knights of Vengeance, from this season's BigBad, 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 position of BigBad by tricking her into giving up her powers. After Nerissa later aquired powers of another dimensional Heart, girls grew desperate and decided to [[EnemyMine ally themselves with Phobos]] who is the only person in TheMultiverse capable of taking powers of the Heart against the owner's will. Which of course ended with him stealing Nerissa's powers, taking over his army and deciding to start [[MultiversalConqueror multiversal conquest]]. [[spoiler: At least until Cedric tricked him into giving him all his powers]].
* In the second season finale of ''WesternAnimation/LegionOfSuperHeroes'', [[spoiler: Imperiex, the season'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.]]
* In ''WesternAnimation/BatmanMaskOfThePhantasm'', gangster Salvatore Valestra believes Batman has been murdering his past associates and fears he'll be next. To take out Batman, he turns to another former partner: [[spoiler:the Joker, [[EvilIsNotAToy who murders Valestra himself and uses him as bait for Batman]]]].
* ''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 [[spoiler:[[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.]]