History HijackedByGanon / VideoGames

* 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.

** ''VideoGame/FiveNightsAtFreddys4'' has the Nightmare animatronics, which seem like independent threats due to apparently being dreams. It's then hinted in the next game - and outright confirmed in the tie-in books - that they are Afton's creations and RealAfterAll (though the gameplay itself might be still a trauma-induced reimagination of events; it's ambiguous).

* The ''Franchise/FiveNightsAtFreddys'' franchise: [[BigBad William Afton / "The Purple Guy"]] pulls this one in almost every game of the original series, as pretty much every horror in the series can be linked back to him.

** Seemingly subverted from ''[[VideoGame/FiveNightsAtFreddysVRHelpWanted Help Wanted]]'' and onward: The new BigBad, Glitchtrap, seems to be Afton himself, resurrected as a digital virus. However, it's been heavily implied - especially in tie-in books - that Glitchtrap is actually an advanced AI called [=Mimic1=] that's [[JackTheRipoff pretending]] to be William Afton, who is long dead, which would actually make it a case of Ganon being hijacked by the new villain.

* The ''Franchise/FiveNightsAtFreddys'' franchise: [[BigBad William Afton]] pulls this one in almost every game of the original series, which he even lampshades with his ominous catchphrase "I always come back."
** ''VideoGame/FiveNightsAtFreddys2'' introduces the new, "Toy" counterparts to the animatronics from [[VideoGame/FiveNightsAtFreddys the first game]]. After about two nights of fending them off, the older ones come out and start hunting down the player's office, far more aggressive than the new ones did. Meanwhile, all of the toy counterparts save for Mangle stop attacking almost entirely until the bonus nights. And if that isn't enough, it's also shown that the Toys are attacking you because of what William has done; as in, either he tampered with the animatronics, or they're haunted by a ''[[ThereIsAnother second]]'' set of victims.
** ''VideoGame/FiveNightsAtFreddys3'' gives us Springtrap, the newest BigBad of the game, [[DistantSequel given that everyone else is dead]]. However, it then turns out that he is possessed by William's undead spirit.
** ''VideoGame/FiveNightsAtFreddys4'' has the Nightmare animatronics. Originally, they seem like they have nothing to do with William, partially because they're dreams. And then the next game comes out and reveals that William has monitored the ''[=FNaF=] 4'' bedroom and might have even created the Nightmare animatronics.
** ''VideoGame/FiveNightsAtFreddysSisterLocation'' shows new, futuristic variations of the Freddy Fazbear gang, as well as some new friends. However, all it takes is ''[[ExaggeratedTrope the first cutscene]]'' to reveal they were created by Afton.
** ''VideoGame/FreddyFazbearsPizzeriaSimulator'' has heavily teased Baby, implying she will maintain the BigBad spot from the past game. [[DownplayedTrope And while that is technically true]], she has to share the BigBadDuumvirate with Afton.
** ''VideoGame/FiveNightsAtFreddysVRHelpWanted'' has a somewhat confusing case of this, given that a familiar looking rabbit turns up in the form of Glitchtrap, with the seeming implication of it being Afton himself, having somehow escaped his VideoGame/UltimateCustomNight eternal Hell. However, later installments indicate he was killed off for real, but a digital copy of him is now continuing his work through Vanny, who he possessed and is using to once again terrorize children in VideoGame/FiveNightsAtFreddysSecurityBreach. Both ''Security Breach'''s DLC, ''Ruin'', and the ''Tales From the Pizzaplex'' tie in book series indicate that Glitchtrap is a splinter of The Mimic's code.

** In ''VideoGame/SonicRushAdventure'', Eggman and Eggman Nega, the villains of the first ''VideoGame/SonicRush'', turn out to be the real threat behind Captain Whisker. Many players probably guessed as much the first moment they laid eyes on [[SuspiciouslySimilarSubstitute Whisker]].

** More or less, the ''Castlevania'' series ''runs'' on this trope. If Dracula is not directly mentioned, heard from, or seen, or it is not specifically stated that his followers (most likely [[DragonAscendant Death]], although others have taken up the helm before) are attempting to resurrect him, then there's at least a 90% chance Dracula is ''still'' behind it all. In fact, as ''[[VideoGame/CastlevaniaLamentOfInnocence Lament of Innocence]]'' can attest to, Dracula was hijacking the plot ''[[BatmanGambit before he even]] [[BigBadFriend canonically became Dracula]]''.

** In ''VideoGame/DanganronpaAnotherEpisodeUltraDespairGirls'', Junko {{AI}}s were controlling Shirokuma and Kurokuma, meaning she was manipulating both sides of the entire conflict and is responsible for the Warriors of Hope becoming soldiers of [[ApocalypseCult Ultimate Despair]]. These are then recovered by [[GreaterScopeVillain Izuru Kamukura]], leading to the events of ''2''.

* In ''VideoGame/DarkSoulsII'' both the FinalBoss of the overall game and the ''Crown of the Old Iron King'' DLC, as well as the first boss of the ''Crown of the Sunken King'' DLC, are all revealed to be the LiteralSplitPersonality of the EldritchAbomination [[OmnicidalManiac Manus, Father of the Abyss]] who was the FinalBoss of [[VideoGame/DarkSoulsI the previous game's]] ''Artorias of the Abyss'' DLC and responsible for much of the conflict in the game's background.
* In ''VideoGame/DawnOfWarII: Chaos Rising'', Eliphas was revived by Abaddon to serve Araghast as his 2nd in command. But when the Blood Ravens finally defeat Araghast, he leaves him to die, and takes command of the Black Legion forces. In ''Retribution'', it is revealed that the whole assault on the sub-sector Aurelia was orchestrated by the daemon, inadvertently released by Gabriel back in the end of the first game.
* In ''VideoGame/DawnOfWarIII'', what starts off as a war between the Imperium, Orks, and Eldar quickly devoles into a plot about Eldar reclaiming one of their relics to kill a Greater Daemon of Khorne, even though Daemons weren't present in the start of the game. In a post credits sequence it is revealed that the Necrons are also involved.

** ''VideoGame/KirbyStarAllies'' shows the cloaked figure, Hyness, the clear BigBad, botching a summoning ritual and causing dark hearts to spread across the universe. Throughout the game, the game appropriately builds up the encounter with him, revealing his arsenal, his minions, and his generals before a raid on TheVeryDefinitelyFinalDungeon. However, immediately after a short fight with him where he reveals his true face, he immediately sacrifices himself and his minions to revive his Dark Lord Void Termina, who, while mostly original in appearance, is very heavily implied to be connected to [[VideoGame/KirbysDreamLand2 Dark]] [[VideoGame/KirbysDreamLand3 Matter]] (and [[VideoGame/KirbysDreamLand3 Zero]] [[MonsterProgenitor by]] [[HiveQueen extension]]).
** In ''VideoGame/KirbyAndTheForgottenLand'', after defeating Forgo Leon, the Soul Forgo leaves his body to fight Kirby right before a familiar butterfly flies on their nose and absorbs their power... and then it brings forth the final ''final'' boss of the story: Morpho Knight. It's then subverted as Fecto Forgo then ''survives'' and absorbs Morpho Knight's power, becoming the final ''final'' '''final''' boss, Chaos Elfilis.

* ''Franchise/TheLegendOfZelda'': In multiple games, the hot new BigBad turns out to simply be a pawn of [[TropeNamers Ganon]] or to be [[SealedEvilInACan trying to revive him]]. [[JustifiedTrope Justified]] by the fact that the [[CosmicKeystone Triforce of Power]] gave him ResurrectiveImmortality, and when that fails [[MaouTheDemonKing Demise's curse]] ensures he eventually [[{{reincarnation}} reincarnates]] alongside Zelda & Link.

** ''VideoGame/TheLegendOfZeldaFourSwordsAdventures'' is an odd mixture of this and TheManBehindTheMan. Vaati is a recurring villain from the prequel game ''VideoGame/TheLegendOfZeldaFourSwords'', and is further established in ''VideoGame/TheLegendOfZeldaTheMinishCap'', which was released after ''Adventures''; but about halfway into the game we find out that Ganon is the true villain of the story, just using Vaati as a decoy. In this case, Ganon hijacks the game from the newer villain Vaati, but Vaati has already been established as a villain as an alternate to Ganon, so Ganon becomes TheManBehindTheMan as well.

** ''VideoGame/TheLegendOfZeldaALinkBetweenWorlds'': Zig-zagged. Yuga first appears to be the BigBad, but then Ganon enters the picture, revived by Yuga. Just as you expect him to take the position of BigBad, Yuga absorbs Ganon's power and merges with him before he can do anything, seemingly ''[[DefiedTrope defying]]'' the trope at first. But ''then'', Princess Hilda is later revealed to be [[TheManBehindTheMan The Woman Behind the Man]] all along, and you think Yuga's role as BigBad is going to to stop then and there. Instead, he actually [[TheStarscream betrays Hilda]], turns her into a painting, and absorbs ''her'' power, once again keeping his position. There's also the implication that Yuga is the [[AlternateUniverse Lorule]] counterpart of Ganondorf, meaning that Hilda got hijacked by ''two Ganons at once''.

* ''VideoGame/LittleBigAdventure 2: Twinsen's Odyssey''. Turns out the aliens are just dupes of good ol' Doctor Funfrock.
* In a way, this is played with during the final boss fight of ''VideoGame/MadWorld''. After getting to the final area, you're set to fight the previous champ, and it is never revealed who that is, so one would expect a powerful new face that may reveal something about Jack's past in the games. Then, get ready for this, IT'S THE BLACK BARON. Yes, the guy who died multiple times as a joke character to explain how mini-games work is the final boss and has no clue who Jack is. Oh, and they're surprisingly badass. While the main plot continues as expected, the final boss fight is with the least expected person... but one that has been previously established as a villain of sorts.
* ''VideoGame/MassEffect2'':
** Although it was always pretty obvious, Shepard and co don't confirm the Collectors are working for the Reapers until halfway through the game. Though everyone shrugged and said "It's probably Reapers" in the first conversation about the Collectors. Note that ''VideoGame/MassEffect1'' and ''VideoGame/MassEffect2'' end up presenting the plot twist in the exact same way: by introducing a minor proxy faction as the major antagonist, only for them to turn out and only be a pawn to a greater game. The reveal that the Geth are tools for the Reapers is played up very close to the reveal that the Collectors are tools for the Reapers.
** In a more direct reveal, the main antagonist of ''2'' is Harbinger who is framed as being the Collector General. Only at the end of the game is it revealed that from the very beginning Harbinger was a Reaper which was operating through the General.
* ''VideoGame/MassEffect3'' then follows suit by revealing half-way through that Cerberus and the Illusive Man have become (unwitting) tools for the Reapers as a result of their tinkering with Reaper tech between ''2'' and ''3''.

** ''VideoGame/MegaManX5'' reveals that [[TheVirus the Maverick Virus]] [[PatientZero 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 [[BigBadDuumvirate was working with Sigma during the game]].

** Finally, the ''VideoGame/MegaManZX'' series that continues the ''Zero'' series, the original Biometal W is a part of the Ragnarok space station from ''[[VideoGame/MegaManZero4 Zero 4]]'' and has Weil's consciousness possessing it, driving other Reploids Maverick. It's also implied to have driven the major antagonists of the games into BrainwashedAndCrazy territory by compelling them to carry out its will. Curiously, Master Albert, the BigBad of ''ZX Advent'' and the person who orchestrated the "Game of Destiny" that drives both games, states that ''he'' is the one in control of Model W and not the other way around. With the ''ZX'' series LeftHanging following Albert's demise, it's unknown if he would've been able to back up his claims, though he does show a far greater understanding and application of Model W's powers compared to Serpent, the main villain of the first ''ZX''.

* A complicated quadruple example in the ''VideoGame/MetalGear'' series. In ''VideoGame/MetalGearSolid2SonsOfLiberty'', Revolver Ocelot (already a villain from ''VideoGame/MetalGearSolid'') reveals himself to be a spy for [[AncientConspiracy The Patriots]], but then gets possessed by the hand of Liquid Snake, the BigBad of ''[=MGS1=]'', and goes rogue. Then in ''VideoGame/MetalGearSolid4GunsOfThePatriots'', Liquid seizes control of the SOP system from The Patriots, becoming the BigBad. Then Ocelot reveals that Liquid wasn't possessing him, and that he was working against The Patriots all along.

** In ''VideoGame/TalesOfMonkeyIsland'', [=LeChuck=] is [[BroughtDownToNormal depowered]] and [[HeelFaceTurn turned good]] at the start of Chapter One, and the Marquis De Singe is built up as the main villain, endlessly pursuing Guybrush so that he can use his unique strain of the Pox Of [=LeChuck=] to create the immortality-granting Jus De Vie. However, at the end of Chapter 4, The Marquis suffers DeathByIrony, and [=LeChuck=] reveals that his "good" act was just that, an act, and ''kills Guybrush''.

** In the ''VideoGame/MortalKombat11: Aftermath'' expansion, it seems that [[TimeMaster Kronika]] is the main villain just like in the main campaign, as she needs to be defeated and her crown retrieved before the timeline can be properly restored. However, thanks to being a ManipulativeBastard and TheChessmaster, longtime villain [[EvilSorceror Shang Tsung]] manages to outsmart everyone and become the BigBad for the first time since [[VideoGame/MortalKombat1992 the original arcade game]]: he [[DemotedToDragon demotes his old boss, Shao Kahn, to a Dragon without him realizing it]], [[YourSoulIsMine absorbs Kronika's soul]], and [[GodhoodSeeker uses the crown and hourglass to become the new Keeper of Time]]. It's only thanks to a ''massive'' BatmanGambit from Liu Kang that there's still a chance to stop him, and even '''that''' won't be enough [[TheBadGuyWins if you trigger Tsung's story ending]].
** ''VideoGame/MortalKombat1'' manages to pull this off ''twice:'' the opening cutscene seemingly reveals that Kronika has somehow returned despite being DeaderThanDead and is manipulating this timeline's Shang Tsung and Quan Chi into wreaking havoc. It's eventually revealed that "Kronika" (or rather, "Damashi", as they introduced themselves to Shang Tsung) is actually the Shang Tsung from the bad ending of ''Aftermath'', who is now seeking to rule ''all'' timelines.

** In ''VideoGame/SonicRushAdventure'', Eggman and Eggman Nega turn out to be the real threat behind Captain Whisker.
** In ''VideoGame/SonicGenerations'', Modern Eggman and Classic Eggman are controlling the Time Eater.
** [[DoubleSubversion Double Subverted]] in ''VideoGame/SonicLostWorld''. After losing control of the Deadly Six, he is forced to work with Sonic and Tails. Once the group is defeated, Eggman returns as the final boss.

* ''VideoGame/SpiderManPS4'' has a meta-example of sorts: for most of the game you're fighting against Mr. Negative, a relatively obscure Spider-Man villain (having been first introduced in ''ComicBook/BrandNewDay''), with the threats of Mayor Osborn merely looming over Peter's civilian life. At the same time, Peter's close friend, business partner, and ParentalSubstitute Otto Octavius starts losing his mind over his deteriorating physical health and getting increasingly aggressive in his anger at Osborn, until he finalizes his life's work: a set of powerful robotic limbs and a mind altering cyborg implant to control them. Immediately after, the Sinister Six are assembled, with [[Characters/MarvelComicsOttoOctavius Doctor Octopus]] at the helm.

** It's revealed that, ultimately, the real BigBad was the Iconians, whom ''Series/StarTrekTheNextGeneration'' established as being long extinct. Not only are they not, they are behind most, if not all, of the big conflicts in the game leading up to their defeat. They are even responsible for the Hobus supernova that destroyed Romulus and kickstarted the Kelvin timeline.
** The Dominion are responsible two foes touched upon in the television franchise and who make their grand appearance in the game: firstly the Hur'q who were once a peaceful civilisation turned mindless berserkers, because they were the Dominion's first failed experiment in creating drug-addicted super soldiers; the second enemy are the Fek'Ihri horde, who were the second botched attempt by the Founders to make a subservient soldier race out of the Klingons aeons ago.

** In ''VideoGame/SuperMarioSunshine'', it turns out he's the father of Shadow Mario, a.k.a. Bowser Jr. But Bowser doesn't appear until the final level and acts as the final boss even though Bowser Jr. was [[TheHeavy the main recurring enemy for the entire game]].

** 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.

* In ''Franchise/{{Tekken}}'', RogueProtagonist Kazuya Mishima seemingly kills his ArchnemesisDad Heihachi at the end of the first game, only for Heihachi to return as the ''protagonist'' of the sequel before acting as the BigBad for virtually the entire series. Heihachi is finally KilledOffForReal in ''VideoGame/Tekken7'' after being thrown into a volcano (following being thrown off a cliff ''[[RasputinianDeath twice]]'').

** The TrueFinalBoss of the ''Burning Crusade'' expansion is Kil'jaeden the Deceiver, one of the arch-demon lords of the Burning Legion and the mover behind most of the events of the expansion. However, his appearance in the final content patch came as a surprise to almost everyone, since all of the promotion for ''BC'' was focused on the confrontation with Illidan. Even the mighty Kael'thas Sunstrider was seen as something of a throwaway boss -- a stepping stone to Illidan -- until it was revealed that he was acting as a SycophanticServant for Kil'jaeden.

** The Jailer in the Shadowlands expansion at first only appears to hijack the Lich King. Having pulled various strings that saw the creation of the Scourge, the Lich King himself, and various other loose threads that were left in the two previous expansions. As the expansion progressed, it was revealed that the Dreadlords were his agents the whole time, with various Legion-related plot threads and characters being his own gambits and he successfully hijacked the Biggest Bad title from the Legion itself.

* The end of the Nod campaign in ''VideoGame/CommandAndConquerTiberian Sun: Firestorm'' reveals that CABAL was made from Kane's consciousness.

* In ''VideoGame/CommandAndConquerRedAlert3'', the newly introduced faction, the Empire of the Rising Sun, is treated as an emerging threat, enough to catch both the Soviets and the Allies by surprise. It's so bad that in the Allied campaign (and the Imperial one, for that matter), the Allies and Soviets sign an uneasy alliance in order to fight off the Japanese army. However, in both the Soviet and Allied campaigns, the Empire is swiftly pacified in the seventh mission in a nine mission campaign. The remaining two missions involve the Allies and Soviets fighting each other as they did before, both in this game and previous entries.

* In ''VideoGame/BaldursGateIII'', [[spoiler:not only is GodOfEvil Bhaal behind everything again (with help from his partners in the Dead Three), but one third of the [[BigBadDuumvirate Big Bad Triumvirate]] is [[VillainousLegacy the granddaughter of Sarevok]], the BigBad of [[VideoGame/BaldursGate the first game]]. This is even [[LampshadeHanging lampshaded]] by TheDon Nine-Fingers Keene, who bitterly states it's always the Dead Three after being told the truth]].

* In the ''VideoGame/MortalKombat11: Aftermath'' expansion, it seems that [[TimeMaster Kronika]] is the main villain just like in the main campaign, as she needs to be defeated and her crown retrieved before the timeline can be properly restored. However, thanks to being a ManipulativeBastard and TheChessmaster, longtime villain [[EvilSorceror Shang Tsung]] manages to outsmart everyone and become the BigBad for the first time since [[VideoGame/MortalKombat1992 the original arcade game]]: he [[DemotedToDragon demotes his old boss, Shao Kahn, to a Dragon without him realizing it]], [[YourSoulIsMine absorbs Kronika's soul]], and [[GodhoodSeeker uses the crown and hourglass to become the new Keeper of Time]]. It's only thanks to a ''massive'' BatmanGambit from Liu Kang that there's still a chance to stop him, and even '''that''' won't be enough [[TheBadGuyWins if you trigger Tsung's story ending]].

* In ''VideoGame/BaldursGateIII'', [[spoiler:not only is GodOfEvil Bhaal behind everything again (with help from his partners in the Dead Three), but one third of the BigBadTriumvirate is the [[VillainousLegacy granddaughter of Sarevok]], the BigBad of the first game. This is even [[LampshadeHanging lampshaded]] by TheDon Nine-Fingers Keene, who bitterly states it's always the Dead Three after being told the truth]].

* The ''Franchise/FiveNightsAtFreddys'' franchise: [[BigBad William Afton]] pulls this one in almost every game of the original series, which he even lampshades with his ominous {{catchphrase}} "I always come back."

** However, the bulk of the game's conflict is about dealing with Blitzkreig, and later on, Entropy - formed when Time Master causes Alchemiss to become corrupted into Entropy.

* Done retroactively in the ''VideoGame/LegacyOfKain'' series. The first game, ''VideoGame/{{Blood Omen|LegacyOfKain}}'', has the BigBad "Hash'ak'gik", while the villains of ''VideoGame/{{Blood Omen 2|LegacyOfKain}}'' (actually [[NonLinearSequel the 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, ''[[VideoGame/LegacyOfKainDefiane Defiance]]'', revealed that Hash'ak'gik and the Hylden Lord were the same being all along. He then partially hijacks ''Defiance'' as well, possessing Janos in the penultimate level and revealing that Raziel's game-long search for how to revive Janos is something he had set up.

* Zig-zagged in ''VideoGame/Persona5Strikers''. The remnants of the Antisocial Force, the main antagonists in ''VideoGame/Persona5'', are the ones who hired Akira Konoe, making them responsible for most of the events of the game. The final boss of the game, having [[DeityOfHumanOrigin evolved]] from [[VirtualSidekick the smartphone app EMMA]] after gaining enough control over the masses, is the Demiurge, which technically makes it different from Yaldabaoth. However, the Demiurge and Yaldabaoth are the same entity in various ideologies, only with a different name. That being said, while both entities have similar motives and are labeled as "false gods" (never mind how EMMA filled the EvilPowerVacuum left behind by Yaldabaoth), they are treated as separate beings, likely because they are based on different interpretations of the Demiurge[[note]]Yaldabaoth is the UsefulNotes/{{Gnostic|ism}} Demiurge, which is portrayed [[GodOfEvil far more malevolently]] than the original Platonic interpretation that influenced what's seen in ''Strikers''[[/note]] -- which probably means something in-universe since the greater ''Franchise/ShinMegamiTensei'' series implies that its FantasyKitchenSink cast of characters [[ClapYourHandsIfYouBelieve is born of the Collective Unconscious of humanity]].

** ''VideoGame/FiveNightsAtFreddysVRHelpWanted'' has a somewhat confusing case of this, given that a familiar looking rabbit turns up in the form of Glithctrap, wiht the obvious implication of it being Afton himself, having somehow escaped his VideoGame/UltimateCustomNight eternal Hell. However, later installments indicate he was killed off for real, but a digital copy of him is now continuing his work through Vanny, who he possessed and is using to once again terrorize children in VideoGame/FiveNightsAtFreddysSecurityBreach. Both Security Breach's DLC, ''Ruin'', and the ''Tales From the Pizzaplex'' tie in book series indicate that Glitchtrap is a splinter of The Mimic's code.

* The ''Franchise/FiveNightsAtFreddys'' franchise: [[BigBad William Afton]] pulls this one in almost every single game, which he even lampshades with his ominous {{catchphrase}} "I always come back."

** Ok, so that's it, Afton was KilledOffForReal in ''Pizzeria Simulator'' and ''VideoGame/UltimateCustomNight'' is his eternal {{Hell}}. There is no way that he would return in ''VideoGame/FiveNightsAtFreddysVRHelpWanted'' to hijack whoever is the villain this time, [[TemptingFate right?]] Wait, who's that yellow rabbit in the corner and why--Ah, goddamit, [[BackFromTheDead he's at it again]].
** He ''was'' killed off for real, but it was his VirtualGhost terrorizing the company in ''Help Wanted'' who's now [[JackTheRipoff continuing his work through]] [[RogueProtagonist Vanessa/Vanny]], who he [[DemonicPossession possessed]] and is using to once again terrorize children in ''VideoGame/FiveNightsAtFreddysSecurityBreach''. [[spoiler:In the GoldenEnding he gets his body back, only to be trapped in the burning pizzeria ''again'' by [[BlobMonster the Blob]].]]

** In ''VideoGame/DanganronpaAnotherEpisodeUltraDespairGirls'', Junko AIs were controlling Shirokuma and Kurokuma, meaning she was manipulating both sides of the entire conflict and is responsible for the Warriors Of Hope becoming soldiers of [[ApocalypseCult Ultimate Despair]]. These are then recovered by [[GreaterScopeVillain Izuru Kamukura]], leading to the events of ''2''.

** ''VideoGame/MetroidDread'' reveals that after losing control on SR-388, the resident Chozo wanted to blow up the planet, restroying both the X parasites and the out-of-control metroids in one fell swoop, but the BigBad prevented it and massacred them instead. This makes said BigBad responsible for the events of the entire series.

* In ''VideoGame/{{Fallout}}'', the Enclave is a GovernmentConspiracy that controlled the United States before [[WorldWarIII its fall]] and turned it into a PeoplesRepublicOfTyranny. In the present day, they still lurk in the shadows after their apparent defeat in ''VideoGame/Fallout2'' trying to reassert their dominance over [[AWorldHalfFull a world that left them behind]].

** In ''VideoGame/Fallout76'' they serve as the GreaterScopeVillain as they created the [[TechnicallyLivingZombie Scorched Plague]] and the [[NuclearMutant Scorchbeasts]] spreading it, almost ending all human life in Appalachia. The player doesn't get to take them down this time, since the cell responsible got themselves killed through their own StupidEvil before the game even began.

* ''Franchise/TheLegendOfZelda'': In multiple games, the hot new BigBad turns out to simply be a pawn of [[TropeNamers Ganon]] or to be [[SealedEvilInACan trying to revive him]].

** In ''VideoGame/RatchetAndClankGoingCommando'', our heroes are offered a job by the CEO of [=MegaCorp=], one of Gadgetron's competitors in the Bogon Galaxy. Their job is initially to recover a stolen prototype, and as the game unfolds, we learn that the CEO is not as kindly as he first appears, and that the prototype will spell doom for the entire universe if unleashed. After fighting their way into his headquarters and confronting him, it's revealed that the CEO was Captain Qwark, the bumbling FakeUltimateHero who served as one of the first game's antagonists, in disguise. Turns out he'd engineered the whole thing in order to save the galaxy from a menace he created in order to be taken seriously as a superhero. Ratchet ends up having to save the galaxy instead after he screws it up.

** In ''[[VideoGame/SonicRushSeries Sonic Rush Adventure]]'', Eggman and Eggman Nega turn out to be the real threat behind Captain Whisker.

* In ''VideoGame/BaldursGateIII'', [[spoiler:not only is GodOfEvil Bhaal behind everything again (with help from his partners in the Dead Three), but one third of the BigBadDuumvirate is the [[VillainousLegacy granddaughter of Sarevok]], the BigBad of the first game]].

** ''VideoGame/TheLegendOfZeldaTwilightPrincess'': After being built up as "The Twilight King" for much of the game, Zant becomes the victim of yet another twist hijack by Ganon. While the appearance of this trope was the cause of debate for years after release, it was already known prior to release that Ganondorf would appear, and the game itself foreshadows (before outright saying) that Ganondorf is the identity of the power-granting god whom Zant reveres.