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Hijacked By Ganon / Video Games

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  • Ace Combat:
    • Played as an Internal Reveal in Ace Combat 5: The Unsung War: the masterminds behind the war between Osea and Yuktobania turn out to be the same rich Belkan nationalists who sponsored the Belkan War fifteen years earlier. However, this was the first time that the Belkan War was even mentioned in the AC canon at that point, and the prequel expanding on it, Ace Combat Zero: The Belkan War, wouldn't come out for another two years.
    • Downplayed in Ace Combat 6: Fires of Liberation. While the main story never reveals it, the designer of the Aigaion Heavy Command Cruiser was a Belkan pilot who defected to Estovakia after the Belkan War, Lorenz Riedel a.k.a. Gault 7. You only find this out by reading the supplementary info. The Aigaion was absolutely crucial to the Estovakian invasion of Emmeria; even if Riedel wasn't actually directing the war, it wouldn't have happened without his involvement.
    • Ace Combat 7: Skies Unknown: Where did Erusea get their super-advanced aerial drone fleet? From Belkans! And the head scientist of the Erusean Air & Space Administration behind the drones is the brains behind the technology, following a spiteful legacy spread by Belkan patriots to cause as much chaos and destruction across the world as they can in revenge for losing the Belkan War.
  • In Baldur's Gate III, not only is God of Evil Bhaal behind everything again (with help from his partners in the Dead Three), but one third of the Big Bad Triumvirate is the granddaughter of Sarevok, the Big Bad of the first game. This is even lampshaded by The Queenpin Nine-Fingers Keene, who bitterly states it's always the Dead Three.
  • In the Batman: Arkham Series, the Joker is always the real Big Bad.
    • 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. But then Strange ends up being a pawn of Ra's, who you already beat earlier in-game, and both of them die 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. The novelization reveals that thanks to Clayface posing as Tyger guards, Joker already had advanced knowledge of Protocol 10 and planned accordingly for it by planning countless explosives beneath Wonder Tower which he would have detonated once Strange killed off all his rivals and he was presumably cured.
    • In Origins, trailers hyped up Black Mask, a relatively unknown villain to non-comic fans, as the Big Bad who hired eight assassins to kill Batman. It was really Joker pretending to be Black Mask the whole time. Joker is arrested and sent to Blackgate Prison at some point while some of his assassins and other villains are still roaming free, but he causes a prison riot and is the final opponent of the main storyline.
    • Unsurprisingly, Knight follows suit: Scarecrow and the Arkham Knight form a Big Bad Duumvirate, but the Joker makes it an Ensemble. 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.
  • Blaster Master Zero III: As the game continues, Jason is led to believe that the Mutant Core from the first game has made yet another comeback. There was a comeback, but it was not the Mutant Core, which stays gone. The actual comeback was done by Planade-G, whose core survived its defeat in the second game and went on to kidnap Eve, subjugating her to gain control of the mutant army. However, at the same time, it's implied Planade-G was attempting to act in what it believed to be Eve's best interests and trying to protect her from any and all perceived threats.
  • BlazBlue has a pretty active Big Bad Ensemble, but ultimately Yuuki Terumi is the overall Big Bad with the largest influence on the plot. He takes center stage in the second game along with his partner-in-crime Relius Clover, but they're both ultimately pushed aside in the third for Hades: Izanami, the goddess of death in the third game and Terumi is rather unceremoniously killed off... except he wasn't. Come the fourth game, both Izanami and their Evil Genius 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 Villain: Exit, Stage Left, leaving Terumi, or rather his true form as Susano'o, as the sole Big Bad and the Final Boss of the series. It's even revealed that Terumi was indirectly responsible for the other villains' plots as well.
  • BoxxyQuest: The Gathering Storm has three examples:
    • The game is purportedly a standalone story, unrelated to its predecessor The Shifted Spires except for a few small nods here and there. Then comes Chapter 7, a flashback Wham Episode dealing with the origins of the first game's Big Bad, Boxxyfan. And then it turns out that the Pale Wraith is his Virtual Ghost, and the sequel's entire plot was set up by him as a gambit to regain his original avatar. He succeeds in the first ending's Stinger, and goes on to fully reclaim his Big Bad status during the True Ending bonus episode. (Let's note that while this is a twist, it's not entirely out of left field — the game comes packaged with a summary of The Shifted Spires' plot, which implies that it's going to be relevant in some way.)
    • Legion is the primary villain of the backstory and Chapter 7, which takes place during said backstory, but seems to disappear from the plot afterwards, his only role being to give Anonymous inner conflict. Then Boxxyfan accidentally revives him and he promptly becomes the final Big Bad, usurping the role from Boxxyfan.
    • Originally Rcoastee, the other Big Bad of the first game, was going to appear in the bonus Easy Mode quest and turn out to be behind the dark happenings, but the quest got cut. However, he does appear in the Alwaysland 2 DLC Bonus Dungeon as a Superboss and attempts to delete Catie and her friends.
  • The Bubble Bobble spin-off 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 Arcade Game Captain America and the Avengers openly presents Red Skull as the Big Bad. The NES version 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 Castlevania games. He's the final boss almost every time, whether he's been visibly in play from the start or not.
    • Symphony of the Night is a classic example; Richter Belmont seems to be the villain, until you find out he was possessed by Shaft from 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 Bad Ending by killing him. And you miss the Inverted Castle, which makes up another half of the game to get to Dracula.
    • Subverted in Aria of Sorrow with a Tomato in the Mirror — you can't expect to fight Dracula if you're playing him, right?
    • Its sequel Dawn of Sorrow deliberately allows you to play this trope straight: fail to equip a certain item before entering the endgame, and Dracula successfully takes over control of your player character, kills off the former main villain, and becomes the Big Bad of Julius Mode.
    • 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 Harmony of Dissonance, which had, as a "novelty" that Dracula didn't appear... He kind of just appears anyway. As a wraith, but still.
    • Castlevania 64: You know that kid Malus? The one who claims he was kidnapped by Dracula's followers along with the other children? He's Dracula. That vampire you fought earlier in the game was a fake.
    • In both Curse of Darkness and Order of Ecclesia, Dracula yet again comes out of nowhere at endgame. This time, it's thanks to Grand Theft Me, although the former is a plan/Thanatos Gambit 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 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 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 Lament of Innocence can attest to, Dracula was hijacking the plot before he even canonically became Dracula.
    • The entire plot of Castlevania: Judgment is preventing Dracula from being Hijacked by Galamoth (of Kid Dracula and SotN fame).
    • Lords of Shadow: Gabriel Belmont was the man who would become Dracula the entire time. Congratulations player! You just hijacked the Big Bad 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 Chrono Cross ends up being Lavos (or, at least, a version of Lavos), just as in its predecessor.
  • In City of Heroes:
    • Nemesis orchestrated the Rikti invasion and possibly the Council overthrow of the 5th Column. However, the events in Cimerora were started by a different group of villains: the Nictus, including Requiem and the 5th Column.
    • The Cimerora zone was only introduced after the appearance of Ouroboros whose chief, Mender Silos, has a Significant Anagram.
    • True veterans of the game know it's only a matter of the time until the writers make Nemesis responsible for all of the Nictus and Kheldian plots entirely as well. The game pokes fun at this. "It's all a Nemesis plot", "Not everything is a Nemesis plot", and "If it wasn't a Nemesis plot already, you can use the Mission Architect to make it one" are all tips on loading screens.
    • The Nemesis version is subverted in the Issue 19 med-porter arc: Your contact realizes the two enemy groups wouldn't work together on their own, and both groups have canonical ties to Nemesis, so he'd be the natural suspect even if he weren't behind everything else. However, it turns out to be Malta pulling the strings.
  • Command & Conquer: Red Alert Series:
    • The end of the Soviet campaign in Command & Conquer: Red Alert reveals that the man secretly advising Stalin is Kane himself.
    • In Command & Conquer: Red Alert 3, 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.
  • The end of the Nod campaign in Command & Conquer: Tiberian Sun: Firestorm reveals that CABAL was made from Kane's consciousness.
  • Commander Keen does this with both major trilogies — it turns out the "Grand Intellect" manipulating the Vorticons is actually Mortimer McMire, Billy Blaze's rival from school. Then it turns out the ruler of the Shikadi, the "Gannalech", is just McMire again (the Shikadi heard "Grand Intellect" but couldn't pronounce it). Also, his babysitter Molly from Aliens Ate My Babysitter turns out to be Mortimer's sister.
  • In Danganronpa, Monokuma/Junko Enoshima will turn out to be the real mastermind even in games which appear to have a different antagonist, which is impressive considering she died in the first game.
  • In de Blob 2, after chasing down Comrade Black to Prisma City in the first chapter, it appears as though the titular Blob will have to deal with another antagonist — Papa Blanc, the mysterious leader of the Blanc cult who rejects color and is running for president. It only takes two more chapters and his victory (via cheating) that he reveals himself to be a disguised Comrade Black.
  • In Dark Souls II both the Final Boss 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 Literal Split Personality of the Eldritch Abomination Manus, Father of the Abyss who was the Final Boss of the previous game's Artorias of the Abyss DLC and responsible for much of the conflict in the game's background.
  • In Dawn of War 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 assault on the sub-sector Aurelia was orchestrated by the daemon, inadvertently released by Gabriel back in the end of the first game.
  • In Dawn of War III, what starts off as a war between the Imperium, Orks, and Eldar quickly devoles into a plot about Eldar reclaiming one of their relics to kill a Greater Daemon of Khorne, even though Daemons weren't present in the start of the game. In a post credits sequence it is revealed that the Necrons are also involved.
  • Who is and isn't a villain in Deus Ex: Invisible War is subject to some interpretation, but it's a major Wham to find out that ApostleCorp is led by JC Denton, the player character from the original Deus Ex.
  • The main antagonist of Devil May Cry 5 is a giant demon named "Urizen" who is trying to use a demonic tree to become stronger. However, newcomer V seems to have a vague connection to him and late in the game it's revealed that he and Urizen are two halves of the same being: the human and demon side of half-demon Vergil, series protagonist Dante's Evil Twin. With his body decaying since his last appearance, Vergil attempted to separate his humanity from his demon heritage but only managed to tear away his conscience from his lust for power. They eventually recombine and Vergil is restored in the climax.
  • Though it was obvious judging by the cover and the title, Diablo turns out to be the real final boss in Diablo III, 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.
  • For most of Dirge of Cerberus, Vincent fights the Tsviets, but the true villain of the story is Hojo, who was possessing Weiss. How well (or not) this was foreshadowed is debatable; the opening cutscene of the game, set during Meteorfall while the non-Optional Party Members of the original game were off fighting Sephiroth, shows Hojo's body mysteriously vanishing, with his only other presence being in flashbacks detailing his past with Vincent and Lucrecia. The game's (defunct) online mode did help to better set up this revelation, but it was only included in the Japanese version.
  • In Divinity: Original Sin II, Bishop Alexandar was built up to be the Big Bad. Then it turns out he was just a Disc-One Final Boss (twice) and the true Big Bad is Dallis the Hammer. But then, it turns out that Dallis was a Big Bad Duumvirate with none other than Rogue Protagonist Lucian. And within the Final Boss 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 True Final Boss. Larian explained Braccus Rex's presence (and foreshadowed it) with him being Back from the Dead by necromancy.
  • King K. Rool (or, as he preferred to be called in this game, Baron K. Roolenstein) in Donkey Kong Country 3: Dixie Kong's Double Trouble! 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.
  • Dragalia Lost has this happen in Chapter 12. Prince Euden and Leonidas had been at war with each other when the void dragons, who up to this point have been Optional Bosses appear and commanded by Phares, the second Scion.
  • The story of Dungeon Master 2: The Legend of Skullkeep appears to be completely unrelated to that of the original game until the cinematic at the very end that reveals that Chaos, the villain from the original game, is really behind it all.
  • In The Exorcism of Annabelle Sunray, The Preacher, the new villain who runs The Church and is trying to keep Annabelle imprisoned, is revealed to be Jason Sunray, Annabelle's abusive father and the antagonist of the first three games.
  • In Fallout, the Enclave is a Government Conspiracy that controlled the United States before its fall and turned it into a People's Republic of Tyranny. In the present day, they still lurk in the shadows after their apparent defeat in Fallout 2 trying to reassert their dominance over a world that left them behind.
  • Far Cry:
  • In Final Fantasy XIV: Endwalker, Fandaniel, one of the main villains of the expansion, is revealed to be Amon, an alliance raid boss fought all the way back in A Realm Reborn. The Amon who was fought in the Syrcus Tower raid is explained to have been a clone body the real deal left behind when he was recruited into the Ascians.
  • In Fire Emblem: Mystery of the Emblem, Hardin is the main antagonist for most of the game, but later it turns out that all of his actions and loss of sanity were orchestrated by Gharnef (The Dragon in the original game), who in turn seeks to revive Medeus.
  • The Five Nights at Freddy's franchise: 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."
    • Five Nights at Freddy's 2 introduces the new, "Toy" counterparts to the animatronics from 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 second set of victims.
    • Five Nights at Freddy's 3 gives us Springtrap, the newest Big Bad of the game, given that everyone else is dead. However, it then turns out that he is possessed by William's undead spirit.
    • Five Nights at Freddy's 4 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.
    • Five Nights at Freddy's: Sister Location shows new, futuristic variations of the Freddy Fazbear gang, as well as some new friends. However, all it takes is the first cutscene to reveal they were created by Afton.
    • Freddy Fazbear's Pizzeria Simulator has heavily teased Baby, implying she will maintain the Big Bad spot from the past game. And while that is technically true, she has to share the Big Bad Duumvirate with Afton.
    • Five Nights At Freddys VR Help Wanted 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 Ultimate Custom Night 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 Five Nights at Freddy's: Security Breach. 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.
  • Zig-zagged with Freedom Force 2:
    • Nuclear Winter was the Starter Villain in the first game, but here he returns as the second game's Starter Villain and uses Time Master's inert body to steal nuclear weapons.
    • 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.
    • The heroes are forced to use Time Master as an Enemy Mine; and of course once Entropy is defeated, Time Master acts as the game's final boss. Time Master wasn't so much behind what happened in the second game so much as he used the events as an opportunity to sneak out, similar to how some comic books depicted some villain(s) returning to evil.
  • Freedom Planet 2: Merga is the primary villain for the majority of the game's story, but ultimately steps down from using Bakunawa to harvest Avalice's moon once Pangu plays a distorted recording of Cordelia; her long lost love. Just then, Syntax (an affiliate of Lord Brevon from the previous game) shows up on-screen and uses Code Black 2.0 to resume Merga's original plan, forcing the heroines to put a stop to her; later being aided by Merga herself during the fight against Bakunawa Fusion.
  • In Fullmetal Alchemist 2: Curse Of The Crimson Elixir, the game's Big Bad is a former state alchemist named Crowley who uses an army of alchemical Golems throughout the story which he controls through a Philosopher's Stone in a ruined nation. In the post-credits scenes, Envy, Lust, and Gluttony talk about the situation, revealing they manipulated Crowley toward finding the stone to bring back his dead lover, although unlike most of their meddling they underestimated Crowley and lost control of the situation. However, they (and as a result likely Dante) still served as the Greater-Scope Villain and the true instigator of the events.
  • Zig-zagged in Golden Sun: Dark Dawn, since the recurring baddie is openly hanging out with the new baddies, in a Paper-Thin Disguise, for much of the game. However, all the characters believe him to have been dead since the last game, so it's a shock to them when his identity is revealed. He laughs. And this being Alex, we still don't even know what he's after, nor do we get to beat him down for it. In a sense, it's played straight. At first, it seems like you're going to stop the Psynergy Vortexes and get the roc feather, but the Vortex subplot is dropped after Konpa Cave until The Stinger, and the roc feather quest takes a backseat to stopping the Grave Eclipse.
  • In Ikaruga, the Stone-Like from Radiant Silvergun is once again the cause of game's troubles, this time having corrupted Horai into a power hungry dictator and granting her unimaginable powers, and is later confronted as the Final Boss after Tageri is destroyed.
  • Injustice 2: The first Injustice ended with Superman and the Regime getting their collective rear ends kicked, arrested, and humiliated. Now now Brainiac and the Legion of Doom are trying to take over and/or kill everything and the Regime are forced into an Enemy Mine situation with Batman and the other heroes. Did you really think that Superman and the Regime would stop trying to Take Over the World and turn it into a tyrannical Police State where they could annihilate anything they considered a threat to peace (or just plain pissed them off) at will? Yeah... no.
  • Jak 3: Wastelander, it's revealed that Errol from the previous game was turned into a cyborg and is working with the Dark Makers.
  • The King of Fighters: Implied in an ending illustration in The King of Fighters 2002 (which was a plotless Dream Match Game 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 him sitting in a throne surrounded by boss characters from the NESTS Chronicles arc, implying he may have been behind it all. Plausible, as his last canonical appearance in the series ('95) had a version of him with cybernetic implants, white hair, and a darker skin tone compared to his previous appearance in '94 — darker skin and white hair aren't uncommon features of clone characters in the NESTS saga, as isn't cyborg/robotic technology, so the Omega Rugal from '95 could have been a clone, and the real one might still be around. This is given possible support in the console versions of XIII, where Rugal can be seen hacking into the monitors of the SkyNoah, the Cool Airship of his children Adel and Rose, to keep an eye on them.
  • Kingdom Hearts, thanks to its confusing cosmology, has a rather weird example: the Big Bad 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:
    • In the first game, Maleficent was presumed to be the Big Bad 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 Heartless, and his 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 time frame. note 
    • The prequel Birth by Sleep has the elderly Master Xehanort as the main villain, but in the ending he performs Grand Theft Me on Terra, taking over his body to become a new, younger Xehanort, who 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 traveling through time, and all three of them were working on a plan to reform Organization XIII led by a resurrected Master Xehanort commanding them all.
    • Promotional materials for Kingdom Hearts III say that Master Xehanort is the main villain for the game, making it the first time Word of God doesn't try to hide his involvement. But even then, the events of Kingdom Hearts χ 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 many expected that the trope was set to happen once again in some way. In actuality, it's an inversion, though, as the ending reveals Luxu — better known in the present day as Braig/Xigbar — was manipulating Xehanort the whole time.
    • And for the (presumably) final time, in Kingdom Hearts: Melody of Memory an apparition of Xehanort residing within Kairi's heart serves as the Final Boss.
  • Kirby:
    • While not present in the main story, the Dededetour Mode of Kirby: Triple Deluxe reveals that Big Bad Queen Sectonia was corrupted into villainy by Dark Meta Knight, The Dragon in previous Kirby game Kirby & the Amazing Mirror, via the Dimension Mirror.
    • Kirby Star Allies shows the cloaked figure, Hyness, the clear Big Bad, 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 The Very Definitely Final Dungeon. 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 Dark Matter (and Zero by extension).
    • In Kirby and the Forgotten Land, after defeating Forgo Leon, the Soul Forgo leaves his body to fight Kirby right before a familiar butterfly flies on their nose and absorbs their power... and then it brings forth the final final boss of the story: Morpho Knight. It's then subverted as Fecto Forgo then survives and absorbs Morpho Knight's power, becoming the final final final boss, Chaos Elfilis.
  • In Knightfall: Death and Taxes, it turns out that the Prince of Darkness from the original game is behind the Duke.
  • Done retroactively in the Legacy of Kain series. The first game, Blood Omen, has the Big Bad "Hash'ak'gik", while the villains of Blood Omen 2 (actually 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, 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.
  • The Legend of Heroes: Trails into Reverie: A plot involving strange, artificial duplicates of various characters eventually turns out to itself be helmed by an artificial recreation of the previous game's Big Bad, Ishmelga, inadvertently recreated by a powerful computational system that was simulating alternate timelines; including one timeline where Ishmelga successfully acquired the power of the Great One and fused with protagonist Rean Schwarzer. "Ishmelga Rean" immediately hijacked control of the computational system and began using it in a bid to conquer the continent, much like the real Ishmelga.
  • The Legend of Zelda: In multiple games, the hot new Big Bad turns out to simply be a pawn of Ganon or to be trying to revive him. Justified by the fact that the Triforce of Power gave him Resurrective Immortality, and when that fails Demise's curse ensures he eventually reincarnates alongside Zelda & Link.
    • The Legend of Zelda: A Link to the Past features an odd, ambiguous situation as main villain Agahnim is said, depending on the version, to be either a pawn of Ganon or purposely working for him, yet Ganon directly refers to the dark wizard as his own alter ego right before the final battle (which is supported by an image of Ganon's shadow popping out of Agahnim's body, turning into a bat, and then flying into the Pyramid of Power). If such a claim is indeed true, as further hinted by Agahnim's Leitmotif becoming Ganondorf's theme from The Legend of Zelda: Ocarina of Time onward, Ganon hijacked the game from himself.
    • The Legend of Zelda: Oracle Games: The Twinrova sisters, Kotake and Koume, are the real villains, directing the actions of General Onox and Veran in order to resurrect Ganon. Ganon is the Final Boss, but he does not directly have a hand in the plot, making him more of a Greater-Scope Villain.
    • The Legend of Zelda: Four Swords Adventures is an odd mixture of this and The Man Behind the Man. Vaati is a recurring villain from the prequel game The Legend of Zelda: Four Swords, and is further established in The Legend of Zelda: The Minish Cap, 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 The Man Behind the Man as well.
    • The Legend of Zelda: Twilight Princess: After being built up as "The Twilight King" for half 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.
    • The Legend of Zelda: Skyward Sword: Played with in the ending, as while Ganon doesn't appear in any degree due to the game's placement in the series' timeline (long before the first historical appearance of the Gerudo king in Ocarina of Time), the outcome of the Final Boss battle reveals that the spirit of Ganon, which keeps pursuing Zelda and Link's descendants, is the incarnation of the hatred of Demise. In short, every single hijacking Ganon does is also a hijacking by Demise.
    • The Legend of Zelda: A Link Between Worlds: Zig-zagged. Yuga first appears to be the Big Bad, but then Ganon enters the picture, revived by Yuga. Just as you expect him to take the position of Big Bad, Yuga absorbs Ganon's power and merges with him before he can do anything, seemingly defying the trope at first. But then, Princess Hilda is later revealed to be The Woman Behind the Man all along, and you think Yuga's role as Big Bad is going to to stop then and there. Instead, he actually 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 Lorule counterpart of Ganondorf, meaning that Hilda got hijacked by two Ganons at once.
    • Hyrule Warriors: Zig-zagged but ultimately played straight in the game. The apparent Big Bad at the start of the game is Cia, a corrupted witch and Anti-Villain. It's soon revealed that the driving force behind her corruption was none other than Ganondorf himself. However, his initial attempt to hijack the plot is thwarted when he tries to pull a You Have Outlived Your Usefulness 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 Big Bad after all, but Ganon takes advantage of her conflict with the heroes to restore his full power and promptly takes over again after they've dealt with her. In an amusing twist from the usual, the game lets you play as him as he performs the hijacking. The game has a bit of a Leaning on the Fourth Wall moment when Ganondorf first reveals himself, as he says Cia was his "favorite puppet yet."
    • Cadence of Hyrule:
    • Hyrule Warriors: Age of Calamity plays around with this trope, but ultimately plays it straight. Harbinger Ganon is a dormant version of Terrako from the new timeline that is corrupted by Malice brought when the Terrako of the main timeline jumped into the past to try and change it, becoming Ganon's vessel in the process. Meanwhile, Astor perfectly knows that he's working for Calamity Ganon, but he sees the Calamity as an extension of himself, lending it the power to destroy Hyrule and then rule the world. When Astor ends up being defeated in the battle in Hyrule Castle, Harbinger Ganon puts him in his place by quite literally hijacking Astor's body and then using it to form Calamity Ganon itself, due to Astor's repeated failures and having the gall to order Ganon around.
    • Even Ganon himself isn't immune to being hijacked. In Soulcalibur II, Link's character profile explains that he came to the Soul universe as a Guest Fighter because he discovered that a sorcerer he defeated, very strongly implied to be the Ocarina of Time incarnation of Ganondorf, was under the influence of the evil sword Soul Edge.
  • Little Big Adventure 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 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.
  • Mass Effect 2:
    • 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 Mass Effect and Mass Effect 2 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.
  • Mass Effect 3 then follows suit by revealing half-way through that Cerberus and the Illusive Man have become (unwitting) tools for the Reapers as a result of their tinkering with Reaper tech between 2 and 3.
  • After defeating Lord Bane in Maximo vs. Army of Zin, Maximo learns that the title army was awakened by the ghost of King Achille, main villain of the first game.
  • This is the trademark tactic for Dr. Wily and Sigma in the Mega Man series.
    • Wily pretended to reform in Mega Man 3, and in all subsequent main series games except Mega Man 7, Mega Man 8, and Mega Man 11, he turns out to be using the initial villain or some other phenomenon as a decoy. He also does it in Mega Man V for the Game Boy with the Stardroids, though in a bit of a twist, he is not the final boss of the game. Amusingly, Mega Man 9 and Mega Man 10 don't even try to hide that he's the final boss in those games, as the achievement for beating each game is "Whomp Wily!"
    • Super Adventure Rockman is also a rare exception, where Wily sets up the Big Bad but loses control of it, a la Mega Man V.
    • A lot of fan games that have Wily as the Big Bad of the game, like Mega Man Unlimited and Mega Man Super Fighting Robot, also go this route, though the latter has Mega Man see this trope coming.
    • In the Mega Man X games, Sigma hijacks all the main villains from Mega Man X2 onward, to the point it's a twist that he isn't the Big Bad of Mega Man X8 (though the plot point of New Generation Reploids having Sigma's DNA in their Copy Chips as well as Lumine more or less carrying out Sigma's plans means he's instead a Greater-Scope Villain). This gets lampshaded in Mega Man X4 when Split Mushroom responds to a demand to reveal the mastermind behind the game's plot with the meme-tastic "Take a wild guess", after which his lifebar, carrying Sigma's logo, appears, unlike members of Repliforce. note  It's also subverted in Mega Man X6, where the Big Bad was not Sigma; it was Gate, and Gate resurrected Sigma to use him to destroy X, but Sigma Came Back Wrong (due to stretching himself too thin when he spread the Sigma Virus over the entire planet) and was obviously not the controlling force behind the plot. Even so, despite being the Reploid equivalent of a Revenant Zombie and only slowly regaining coherence as time passed, Sigma drops this line upon revealing himself and offing Gate in the process.
      Sigma: Oh please. I did not die. Nor did I need your help! Now get lost!
    • Mega Man X5 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 Word of God has stated that yes, Wily was still alive and was working with Sigma during the game.
    • Due to his hand in the creation of the Maverick Virus and Zero, Wily also indirectly set up the events of the Mega Man Zero 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 Big Bad of the Zero series, uses a robot (Zero's original body, specifically) that Wily built.
    • Dr. Weil himself pulls this off. The first two Zero games each have different villains, but ultimately Weil (who only first appears in the third game) is the Greater-Scope Villain for both. He even resurrects one of the previous main villains (Copy X) as a Puppet King and Disc-One Final Boss, if only to further his plans.
    • Finally, the Mega Man ZX 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, driving other Reploids Maverick. It's also implied to have driven the major antagonists of the games into Brainwashed and Crazy territory by compelling them to carry out its will. Curiously, Master Albert, the Big Bad 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 Left Hanging following Albert's demise, it's unknown if he would've been able to back up his claims, though he does show a far greater understanding and application of Model W's powers compared to Serpent, the main villain of the first ZX.
    • In the Mega Man Battle Network games (which are an Alternate Timeline 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, making it actually effective when he appears in 6 and reveals his Evil Plan. However, the villain of 4 and 5 is the organization Nebula, led by Wily's son.
    • Even X-series fan games get in on it. Mega Man X: Mavericks continues the tradtion of Sigma being behind everything, so there's no point in spoilering it. That being said...
      • In the third game, Sigma is working with Dr. Weil. Sigma ends up getting taken out and Dr. Weil becomes the sole bad guy for the rest of the game. This trope kicks in when after the final battle, we find that Dr. Weil had been possessed...
      • In the fourth game, X is so sure that Sigma is behind Gate's plans that he already starts asking the bosses about it before reaching the fortress. He's right, of course, but Sigma was only brought back thanks to the Stardroids, who were under the leadership of the real bad guy responsible for everything: Dr. Wily.
  • A complicated quadruple example in the Metal Gear series. In Metal Gear Solid 2: Sons of Liberty, Revolver Ocelot (already a villain from Metal Gear Solid) reveals himself to be a spy for The Patriots, but then gets possessed by the hand of Liquid Snake, the Big Bad of MGS1, and goes rogue. Then in Metal Gear Solid 4: Guns of the Patriots, Liquid seizes control of the SOP system from The Patriots, becoming the Big Bad. Then Ocelot reveals that Liquid wasn't possessing him, and that he was working against The Patriots all along.
  • Inverted in the second Metal Slug game, where Morden is hijacked right at the end by the 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 Big Bad unrelated to any of the previous games, and in the sixth game, where the Martians' plot (working once again with Morden) is hijacked by a Martian-eating race of aliens, forcing an Enemy Mine between the heroes, the Rebel Army, and the Martians.
  • Metroid:
    • In Metroid Prime 2: Echoes, the Ing are the villains for most of the game, with the player occasionally running into the mysterious Dark Samus, who has her own agenda given how she'll even attack Ing. Dark Samus is actually the resurrected/reincarnated form of Metroid Prime, the Final Boss of the first game, and hijacks the role of True Final Boss by trying to kill Samus after she defeats the Emperor Ing and the whole Dark World is collapsing around them. She goes on to take the starring role as the Big Bad of Metroid Prime 3: Corruption, making her the overarching villain of the Prime subseries.
    • In Metroid: Other M, the events aboard the Bottle Ship are the fault of MB, who is essentially a resurrected Mother Brain. The postgame is a more jarring and unexpected example. Remember Phantoon? A boss who only appeared in Super Metroid 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 Greater-Scope Villain.
    • In Metroid II: Return of Samus, the Final Boss is the Metroid Queen. In the 3DS remake, Metroid: Samus Returns, Samus' nemesis Ridley is tacked on at the end, as a closer tie-in to the chronological follow-up, Super Metroid.
    • Metroid Dread reveals that after losing control on SR-388, the resident Chozo wanted to blow up the planet, destroying both the X parasites and the out-of-control metroids in one fell swoop, but the Big Bad prevented it and massacred them instead. This makes said Big Bad responsible for the events of the entire series.
  • Monkey Island:
    • Subverted in Escape from Monkey Island, where after a lot of buildup for the anti-pirate business tycoon Ozzie Mandrill as the new villain, LeChuck appears... and it turns out he's working for Mandrill, who really is the new villain.
    • In Tales of Monkey Island, LeChuck is depowered and 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 Death by Irony, and LeChuck reveals that his "good" act was just that, an act, and kills Guybrush.
  • Mortal Kombat:
  • In Naruto: Clash of Ninja 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 her Dragon, Bando, who in turn was manipulated by Kabuto for unknown reasons (it's unclear whether he did it on his own, or for Orochimaru).
  • Ninja Gaiden II on the NES spends a lot of time building up Ashtar, the self-proclaimed "Emperor of Darkness," as the Big Bad. 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 Not Quite Dead to become the main villain.
  • Oddworld:
    • Oddworld: Abe's Exoddus features the Magog Cartel as the primary villains, lead by the Big Bad Triumvirate of Vice President Aslik, General Dripik and Director Phleg. Partway through the game, however, it's revealed that Molluck, the Big Bad of Abe's Oddysee, was their boss. It's subverted by the fact that he was killed off at the end of Oddysee. Since so little time — probably a week at most — passes between the two games, and Exoddus shows that his ex-Dragons are still dealing with the fallout of his death, he was ultimately responsible for everything that takes place in both games, despite not having a direct hand in the sequel's events.
    • Played straight in the remake, Soulstorm. Molluck is alive and well, having somehow survived the ending of the first game.
  • One Piece: Pirate Warriors 4 includes a version of the manga's Wano arc that diverges heavily because Wano was nowhere near finished at the time. As a result, Blackbeard is brought in and hatches a scheme to take Kaidou's head and claim the Big Bad seat for himself. A scheme which ultimately fails because taking the head of the World's Strongest Man who survived multiple guillotines isn't the easiest thing to do. And when a pissed off Kaidou arrives, Blackbeard decides to make himself scarce.
  • Zig-zagged in Persona 5 Strikers. The remnants of the Antisocial Force, the main antagonists in Persona 5, 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 evolved from 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 Evil Power Vacuum left behind by Yaldabaoth), they are treated as separate beings, likely because they are based on different interpretations of the Demiurgenote  — which probably means something in-universe since the greater Shin Megami Tensei series implies that its Fantasy Kitchen Sink cast of characters is born of the collective unconscious of humanity.
  • Phantasy Star:
  • Pokémon:
    • Pokémon Ultra Sun and Ultra Moon 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 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.
    • Before that, Pokémon Omega Ruby and Alpha Sapphire played this more straight. After catching Rayquaza, the original character Zinnia fights the player one last time. It almost seems like she's the final boss of the game, at least until the player and Rayquaza destroy the meteor. And from its fragments comes the real final boss of the game: Deoxys!
  • In Project × Zone 2, the Final Boss, Byaku Shin, is actually a revived Kyuju Kyu, who was originally the true Big Bad from Namco × Capcom.
  • Ratchet & Clank:
    • 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, Tools of Destruction, and in the sequel, Quest for Booty, Slag from the last game gets an upgrade to become the new villain. All of that, however, is thrown right out the window when the end of the game reveals that the entire subplot regarding Clank and the Zoni (which turns out to be the real plot of the game) was actually set up by Dr. Nefarious, from Up Your Arsenal. This trope would then be inverted in All 4 One, however.
    • In Ratchet & Clank: Going Commando, 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 Fake Ultimate Hero 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 Qwark screws it up.
    • Ratchet & Clank (2016) does this in both game and movie form. A retelling of the first game, one of the many additions to the cast is none other than Dr. Nefarious, who originally hadn't shown up for another two games, and as noted above had become quite a bigger player in the series since. Three guesses what happens...
  • Averted in Resident Evil 7: Biohazard. The Umbrella Corporation doesn't have anything to do with this incident at all, and in fact their only presence is through a new company called Blue Umbrella, made up of former employees who joined forces with the B.S.A.A. in the intervening years between 6 and 7 to atone for the original company's various wrongs. While the H.C.F. (a task force under the control of Wesker after he split off from Umbrella) is mentioned in files as having collaborated on the project that led to the "birth" of Eveline, it's unknown if Wesker himself, who was Killed Off for Real in Resident Evil 5, had any direct involvement.
  • ROBO OH involves an alien giant robot named Maxcyber luring other robots into a tournament in hopes of absorbing their abilities. If the player refuses to use the powerups granted by the villain after each match, Maxcyber is suddenly usurped by Shippo, a Guest Fighter from Uchu Mega Fight. Once both of Shippo's giant machines are destroyed, however, Maxcyber returns and drains the giant Shippooh to become Dimcyber. He then faces the player character as the True Final Boss.
  • In RosenkreuzStilette Freudenstachel, Iris Zeppelin, who instigated the war between RKS and the Church in the first game, is revealed to be behind the Dark Magi and Spiritia's kidnapping, having been posing as the Pope via a homunculus. Probably not a huge surprise, considering what this game is a homage to.
  • Happens twice in the Skylanders series.
    • Zig-zagged in Swap Force, where the franchise's Big Bad Kaos was the main antagonist throughout the whole game and the hijacking only happens before the final level. After his recent plan has been foiled and he's captured by the Skylanders, his mother Kaossandra comes in to free him and kidnap Tessa. When the Skylanders head to their hideout to defeat Kaossandra and rescue Tessa, Kaossandra announces herself to be a greater Portal Master than her son and that she's gonna claim all of Skylands for herself. But after she's defeated by getting trapped in a mirror prison, Kaos takes the title of Big Bad right back by going behind his mother's back. Kaossandra, however, isn't upset about this and is instead proud of her son.
    • The following game, Trap Team, plays this a lot more straight. The main villains of the game are the Doom Raiders, some of the most notorious villains Skylands has ever seen. They threw Kaos under the bus after he freed them, which in turn made Kaos do the unthinkable and team up with the Skylanders to take all of the Doom Raiders down. When the leader and last remaining one, the Golden Queen has been captured, it looks like things are over until the people at Skylander Academy realize that Kaos is nowhere to be found. Turns out he's now controlling the Ultimate Weapon that the Doom Raiders had built to once again try to conquer Skylands for himself, meaning he's the final boss of a Skylanders game yet again.
  • Sly Cooper subverts this:
    • The second game centers around the robotic body parts of previous Big Bad Clockwerk, and Sly's attempts to destroy them and make sure he can never threaten anyone again. Clockwerk's body is reassembled in the final level... and it turns out that Arpeggio doesn't want to resurrect the old owl, just use his body to become immortal. Even when Clockwerk comes alive again, it's not his mind in the metal body, but Neyla's. Just to drive the point home, the final scene has Carmelita destroy a vital component that renders Clockwerk Deader than Dead.
    • Clockwerk's appearances in Sly Cooper: Thieves in Time also subvert this; they have nothing to do with the plot, simply serving as Easter Eggs to observant players.
  • Sonic the Hedgehog:
    • In Sonic Rush Adventure, Eggman and Eggman Nega turn out to be the real threat behind Captain Whisker.
    • In Sonic Generations, Modern Eggman and Classic Eggman are controlling the Time Eater.
    • Double Subverted in Sonic Lost World. After losing control of the Deadly Six, he is forced to work with Sonic and Tails. Once the group is defeated, Eggman returns as the final boss.
  • In Steve Meretzky's Spellcasting 201 (an Interactive Fiction game published by Legend Entertainment), the villain of the game turns out to be the villain of the previous game, Spellcasting 101, (the evil stepfather of the protagonist) in disguise. The same trick is pulled in the sequel, Spellcasting 301, and it's done with an even more heavy-handed joke: it turns out that the father disguised himself as a ridiculously hot woman. Talk about having it in for your son...
  • Spider-Man (PS4) 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 Brand New Day), with the threats of Mayor Osborn merely looming over Peter's civilian life. At the same time, Peter's close friend, business partner, and Parental Substitute 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 Doctor Octopus at the helm.
  • Star Fox Adventures: Andross ends up hijacking General Scales, and his power is the main reason why Scales managed to amass so much power and influence to become the tyrannical ruler of Sauria in the first place. You even have to beat him the same way as in Star Fox 64. The hints foreshadowing Andross' return are scarce (due to the game's difficult development cycle), but they exist. Namely...
  • Star Trek Online:
    • It's revealed that, ultimately, the real Big Bad was the Iconians, whom Star Trek: The Next Generation established as being long extinct. Not only are they not, they are behind most, if not all, of the big conflicts in the game leading up to their defeat. They are even responsible for the Hobus supernova that destroyed Romulus and kickstarted the Kelvin timeline.
    • The Dominion are responsible two foes touched upon in the television franchise and who make their grand appearance in the game: firstly the Hur'q who were once a peaceful civilisation turned mindless berserkers, because they were the Dominion's first failed experiment in creating drug-addicted super soldiers; the second enemy are the Fek'Ihri horde, who were the second botched attempt by the Founders to make a subservient soldier race out of the Klingons aeons ago.
  • Emperor Tenebrae/Vitiate/Valkorion in Star Wars: The Old Republic. As the leader of the True Sith Empire he serves as the Big Bad for the game and the Greater-Scope Villain of the Old Republic saga overall. However, after being defeated by the Hero of Tython (Jedi Knight class) he returns as the Greater-Scope Villain of the Shadow of Revan expansion before coming back to life for the Eternal Throne and Fallen Empire expansions to serve as the Big Bad for those. He's finally Killed Off for Real in the Onslaught expansion after four attempts within the same game.
  • Super Mario Bros.: Bowser tends to take centerfold whenever he's not the Big Bad of some games.
    • In Super Mario Sunshine, it turns out he's the father of Shadow Mario, a.k.a. Bowser Jr. But Bowser doesn't appear until the final level and acts as the final boss even though Bowser Jr. was the main recurring enemy for the entire game.
    • Bowser has been doing this since he was baby, taking over the main antagonist spot from Kamek in Super Mario World 2: Yoshi's Island. However, this doesn't prevent adult Bowser himself from making surprise appearances in some of the Yoshi's Island games as well. Yoshi's New Island has him bending space-time just to become the Final Boss of the game, meaning that he hijacks his own younger self.
    • Averted, but attempted in Paper Mario: The Thousand-Year Door, where Bowser is not the main antagonist. He and Kammy Koopa appear in several cutscenes seeking the Crystal Stars, but always arrive after Mario and company have left with the Stars. In the climax, Bowser drops in — literally — during the confrontation between Mario and Grodus (the essential main antagonist), and then the player has to fight Bowser and Kammy. But once the player defeats Bowser and Kammy, it turns out that Grodus took advantage of the distraction to grab Peach and take her to the next chamber. So in the end, Bowser doesn't hijack the plot. He never even finds out what's going on, and ends up being little more than comic relief in the otherwise serious endgame.note 
      Bowser: What's a finale without a Bowser appearance, huh? A cruddy finale, that's what!
    • In Mario & Luigi: Partners in Time, Bowser isn't the Big Bad. Once the battle against The Shroobs is finished, Bowser becomes the Post-Final Boss after being given a power boost.
    • In Mario & Luigi: Dream Team, the supposed Big Bad, Antasma, forms an alliance with Bowser, but Bowser, under the impression that Antasma was planning to betray him (and uninterested in sharing victory with him anyway), betrays Antasma first.
    • Luigi's Mansion subverts this. The game implies about 3/4 of the way through that Bowser is going to hijack the plot. At the end of the game, the final boss, King Boo, flies into a Bowser portrait and sucks Luigi in, teleporting him to the roof of the mansion, where Luigi is pitted against what appears to be Bowser. However, "Bowser" is revealed to be nothing more than a hollow puppet being controlled by King Boo. Bowser himself has no part in it.
    • Luigi's Mansion: Dark Moon 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. The player, on the other hand, knows this from the start.
    • In Dance Dance Revolution Mario Mix, 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.
    • Mario + Rabbids Kingdom Battle zig-zags the trope. The game sets up Bowser Jr. as the main antagonist, only for both him and the player characters to find out that Bowser will be coming home early. By the time the player reaches Bowser's Castle, Bowser has been defeated and possessed by the Megabug that was a constant yet ignored presence throughout the entire game.
  • Super Robot Wars:
  • Super Smash Bros.:
    • Although Master Hand is the flagship Final Boss in the series, it subverts this trope in The Subspace Emissary. After Bowser, Wario, and the Ancient Minister have been causing most of the trouble, Ganondorf is revealed to be in charge of them behind the scenes. However, Ganondorf is himself taking orders from Master Hand, only to find that yet another villain was controlling Master Hand the whole time.
    • Used in Sephiroth's reveal trailer for Super Smash Bros. Ultimate. It opens with the assembled fighters attempting to fight back against Galeem, the Big Bad from the game's story mode. However, just as it's about to launch a final attack, it suddenly gets sliced in half. The monster disintegrates, revealing Sephiroth to be its killer; he then assaults the fighters, going after Cloud in particular.
  • In System Shock 2, you initially believe that The Many is the Big Bad, having hijacked the Von Braun's crew with mind control. Then your Mission Control turns out to be SHODAN from the previous game, who is revealed as the creator of The Many. After you wipe out her creation, SHODAN becomes the villain, though the box art and intro might have given it away. This is partly because SS2 was meant to be a new standalone game, with the System Shock elements bolted on afterwards.
  • In Tekken, Rogue Protagonist Kazuya Mishima seemingly kills his Archnemesis Dad Heihachi at the end of the first game, only for Heihachi to return as the protagonist of the sequel before acting as the Big Bad for virtually the entire series. Heihachi is finally Killed Off for Real in Tekken 7 after being thrown into a volcano (following being thrown off a cliff twice).
  • In Time Crisis: Project Titan, Ricardo Blanco is set up to be the Big Bad, being the one responsible for framing Richard Miller for assassinating the president of Caruba, Xavier Serrano, but after defeating Ricardo, Wild Dog comes in and kills Ricardo, making Wild Dog the true Big Bad of Project Titan.
  • TRON 2.0: Okay, so we have Thorne causing massive viral outbreak all over cyberspace, 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, 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 TRON film! note 
  • Boss Cass, the Big Bad in Ty the Tasmanian Tiger 1 and 2, is presented as The Quisling (though, like Black Mage, this would imply he'd never been on "Team Evil") with 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.
  • Valkyrie Profile 2: Silmeria is hijacked at the end by Lezard Valeth, who had been a party member for most of the game, thus giving the impression he was a different person entirely from 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.
  • Ubersoldier seemingly ends with the Nazi Mad Scientist Big Bad, Dr. Schaeffer, being killed, and the sequel sees a new rogue Ubersoldier unit hell-bent on taking over Europe. But after defeating the villain who's supposedly the Ubersoldier commander, it turns out he's working for Dr. Schaeffer, who survived being shot in the previous game.
  • With no real buildup 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 Virtua Cop 3, the leader of the terrorist organization is revealed to be none other than Joe Fang, who was thought to have been killed twice.
  • Virtue's Last Reward:
    • Nine individuals are placed in a Nonary Game, similar to the first game, except instead of the person Zero, they are now being watched over by an A.I. rabbit named Zero III. As it turns out, both Zero III and his creator, the future Sigma Klim, are working with the original Zero, Akane Kurashiki. The game attempts to persuade the player early on that this isn't the case, with characters commenting on how the first Zero already got what they wanted.
    • In addition, the other antagonist, Dio/Left, is revealed to be a member of the same cult that Ace/Gentaro Hongou, one of the villains of the original game, was from.
  • Warcraft pulls this with the Burning Legion. The Legion is behind everything bad that happens in all three strategy games, one way or another. Similarly, the Legion is what ties together many of the plot threads in Classic World of Warcraft, though that game also sets up the threat of the Old Gods. Warcraft III subverts it, as the Lich King becomes un-hijacked and the Legion's attempt to re-hijack him fails.
  • In Wasteland 2 the True Final Boss is the Base Cochise A.I., the Big Bad from the first game that Matthias was trying to resurrect and ended up getting controlled by.
  • The Prophets from Wild ARMs 3 spend most of the game working to bring an ancient demon back to life. They succeed and Siegfried (heavily implied to be Zeikfried from the first game), comes back from the dead to continue his conquest of Filgaia by terraforming it into a demon planet, and then aiming to use it as a starship to do battle with other worlds.
  • World of Warcraft:
    • The True Final Boss 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 Sycophantic Servant for Kil'jaeden.
    • The Warlords of Draenor expansion started with a time-travelling Garrosh convincing his father to reject the demonic influence of the Burning Legion. The players must travel to this alternate timeline and fight back against the orcs' new Iron Horde, which is stronger than ever due to them imprisoning the Legion's emissary Gul'dan and embracing superior technology instead of fel magic. However, the expansion somehow ends up with Gul'dan back on top and the players battling the demonic hordes yet again. This continued into the following expansion, Legion.
    • 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.
  • In Zero the Kamikaze Squirrel, the mastermind behind Jaques Le Sheets' scheme is Edgar Ektor, the Big Bad of the overall Aero the Acro-Bat series.

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