Hijacked By Ganon / Anime & Manga

• Batman Ninja: The climactic battle involves Gorilla Grodd revealing that he had turned all of the Batman villains that travelled with him to the past into Manchurian Agents that would subconsciously create individual parts of a Steampunk Humongous Mecha that they would then hand over to him so he would Take Over the World... a plan that worked perfectly okay, except that it turns out The Joker shook off the mind control very early and so he appears with a new part that allows him to take over the mecha, which he will use to raise apocalyptic levels of hell on Japan for fun. Result: Grodd ends up teaming up with Batman to put a stop to this menace.
• Case Closed: Downplayed example in the Non-Serial Movie Detective Conan Film 05: Countdown To Heaven: after the villain of the film (an artist turned Mad Bomber who went on an explosive killing spree to get back at the people who built an apartment tower blocking his view of Mount Fuji) is arrested, the Black Organization makes a quick yet notable appearance by setting said tower on fire to try to kill Conan and his friends, enabling the climactic Homage to The Towering Inferno. Ironically, the protagonists initially suspected the Black Organization to be behind the murders, but dismissed it as paranoia.
• In Codename: Sailor V, some of this happens once Sailor Moon begins to run concurrently. Suddenly the Dark Agency was a branch of the Dark Kingdom all along.
• Cyborg 009:
  • The majority of antagonists can be traced back to the Black Ghost organization. This is lampshaded in the Devilman crossover when Cyborg 002 correctly guesses that the High-Teen Number Cyborgs are assassins sent by Black Ghost.
  • In the 2001 anime, Skull, the leader of Black Ghost, seemingly dies halfway through the first season. In the "Yomi Kingdom" arc in the second season, it is believed that Van Vogt has become the new leader of Black Ghost. It is later revealed that Skull was still alive and leading the Black Ghost the entire time, and Van Vogt was only the second-in-command of Black Ghost.
• Digimon Adventure 02 has Vamdemon/Myotismon who manipulated Oikawa into the apparent Big Bad of the series who in turn, manipulated Ken into the Digimon Emperor, the villain of the first half of the season. The video games and a little mention in Tamers give this even more of a Mind Screw. The Dark Spore which made Ken the Digimon Emperor came from an attack used by Milleniumon. But Milleniumon is a Jogress Shinka^note DNA Digivolution of a dying Khimeramon and Mugendramon.^note Machinedramon Khimeramon was created by Ken while he was the Digimon Emperor, so Ken actually created his own hijacker while he was hijacked.
• Played with in the Android Saga of Dragon Ball Z: Freeza and his father King Cold appear to the main villains at the very beginning, but they're instantly killed by Trunks who warns them of the real threat: the artificial humans created by Dr. Gero, a former member of the original series' villains The Red Ribbon Army, and whose cyborg Cell serves as the main villain. Gero, however, never made any appearance, nor was he ever mentioned in the original arc.
• Played straight during the Baby Saga of "Dragon Ball GT" when the Tuffle parasite Baby emerges from Dr. Myuu's body and crushes his skull before revealing that everything up to that point was built for his resurrection, including the creation of the bad ol' Doctor as well.
• The manga based on the Galaxy Angel gameverse changed the entire plot of Moonlit Lovers so that Eonia, who was already dead in the game, could be behind it again.
• Getter Robo has the Dinosaur Empire, which acted as the main antagonists of the original manga. In Go, the antagonist is initially the Mad Scientist Professor Lando, but it's then revealed that he's allied himself with the Dinosaur Empire, and in later chapters, the Empire pulls a coup, revealing that he was never truly in control of his army.
• God Mars has President Gihron of Marmelo as the Big Bad of its second arc. He is advised by a mysterious voice that claims he is destined to rule the galaxy. The voice sounds a lot like Zuul, the Big Bad of the first arc. During the final confrontation with Giron, the voice reveals he is Zuul, who has returned to continue his war against the main character, killing Gihron in the process.
• In the Danganronpa Spin-Off manga Killer Killer, it's shown early on that Serial-Killer Killer Takumi became the way he is after witnessing a mass murder at his middle school, with the culprit supposedly still being on the loose. About halfway through it's revealed that the killer was none other than Mukuro Ikusaba, who's been long since dead by the time the manga began.
• The Heaven's Lost Property manga introduces a new evil Angeloid called Siren...who gets killed in about 3 pages by earlier villain Chaos, who then absorbs her powers. Ow.
• In The Kindaichi Case Files, if the murderer of the week sets up a more elaborate plot than usual, there's a good chance that he/she employed the "services" of Yoichi "The Puppeteer from Hell" Takato, Arch-Enemy of series protagonist Hajime Kindaichi. There are also a few Reverse Whodunnit cases where it's clear that Takato is the one pulling the strings, but Hajime still has to figure out the actual murderer.
• An in-universe example in My Hero Academia. We're told for the majority of the series that Tomura Shigaraki has been groomed by All For One from a young age to take his place as The Symbol of Evil. This is supposedly because All For One's body is failing him after his battle with All Might left him half-dead with permanent injuries. Shigaraki has All For One (the superpower, not the man) surgically implanted into his body. This allows All For One to pull a Grand Theft Me on Shigaraki, as it turns out every quirk has the user's consciousness imprinted on it. But then it gets subverted (or possibly enforced if you view Shigaraki as the main recurring villain of the series) when All For One's hold on him gets loosened enough in the final battle for Shigaraki to hijack himself.
• Naruto
  • Orochimaru does this during part one of the anime's interminable filler seasons — they even retcon Mizuki, from the first chapter, into having been operating under the orders of Orochimaru.
  • Zig-zagged with the Akatsuki. First it was revealed that it was all the doing of Jiraiya's former student by name Nagato. But wait, it was actually Tobi, who calls himself Madara but actually he is Obito Uchiha and it was actually real Madara, who manipulated Obito to resurrect him so he could become a god. But wait, later we learn that Obito never had any intention of reviving Madara and planned on using him in order to become a god. But then, rather abruptly, it's revealed that Black Zetsu is doing this to both of them. In fact, he's been manipulating everything connected to the Uchiha and Senju clans since before their founding as part of a ploy to unsealed Kaguya. This includes leading Madara and Obito around by the nose (including somehow tricking Madara into thinking he had created Zetsu), starting the Akatsuki and having Kabuto discover Madara's body.
• In Inuyasha it's almost inevitable that whoever the heroes are fighting next is really a pawn of Naraku. However, to their credit, the heroes are almost always aware of this, increasingly so as the series goes on. And then it turns out Naraku was being manipulated all along by the Shikon jewel — and the ancient dragon youkai inside of it.
• Guile Hideout, the Arc Villain of the Emerald chapter of Pokémon Adventures, is later unmasked to be Archie of Team Aqua, who survived the events of the Ruby and Sapphire chapter. And his armor was given to him by Sird, an Enigmatic Minion previously affiliated with Team Rocket during the FireRed and LeafGreen chapter.
• The US dub of Pokémon Heroes made Annie and Oakley agents of Team Rocket when in the original they had no association with them.
• Puella Magi Madoka Magica's Spin-Off Puella Magi Kazumi Magica. And everyone thought Kyubey's appearence was just a cameo...
• In Puella Magi Madoka Magica The Movie: Rebellion, Kyubey also reveals himself as being responsible for the plot, after having spent the first part of the movie pretending to be a harmless mascot. Ironically, at the end of the movie, he himself is hijacked by Homura of all people!
• Dr. Wily manages to pull one of these off in MegaMan NT Warrior. The 2 beast viruses, Grieger and Falzer, are the Big Bad for the majority of the series until it's revealed that a dead, and reduced to digital form, Dr. Wily programmed and released them on purpose to let 1 kill and absorb the other, thereby creating the ultimate body for him to download himself into.
• A key plot element in Umineko: When They Cry, also inverted:
  • Most of End of the Golden Witch involves Battler trying to keep the role as protagonist and Bernkastel doing the hijacking.
  • In addition, one of the main villains, and the one who gave Beatrice her powers in the first place, Lambdadelta, is shown in a bonus scene to be the one who caused the events of the previous story; and the Big Bad of Higurashi, Miyo Takano, is heavily hinted to be a human incarnation/Alternate Self of Lambda. Ryukishi has denied this, but you never know with him.
• In Zatch Bell!, Riou serves as the main villain for the Faudo arc — until Zeon and Dufaux invade the control room and absolutely crush him. And it happens right after Riou defeats Gash and murders Kiyomaro, too.
• Assassination Classroom:
  • Akira Takaoka is revealed to be the mastermind in the Assassination Island arc, being the one responsible for infecting half of Class 3-E and demanding Nagisa to surrender Koro Sensei to him.
  • Shiro, who is the most frequently recurring villain in the series with the most attempts at killing Koro-sensei, is upgraded to full on Big Bad status with the reveal of his true identity of Yanagisawa, the mad scientist who turned Koro-sensei into a tentacle monster and is indirectly responsible for the moon being destroyed and the death of Aguri.
• In Fairy Tail, the Alvarez Empire is built up as far stronger and far more evil than anything Fairy Tail has ever faced — such an insurmountable force that Makarov disbands the guild rather than face them. However, we later find out that the Emperor of the Alvarez Empire is Zeref, and he is the personal cultivator of this empire from scratch — not because he wants to conquer the world, but because he's hoping that it will put him in a position to bring down Acnologia, a true rotten-to-the-core villain.
• Episode 8 of Phantasy Star Online 2: The Animation reveals that many of the bad things happening are the result of (yet again) another Dark Falz, who is using Darkers to seek out Earthlings that possess high Photon affinity. By kidnapping these Earthlings, it hopes to use one as a vessel to manifest itself and invade Earth. Casra, Quna, and Aika have been working behind the scenes to thwart Dark Falz's plans, and now Itsuki needs to be in on it as well.
• Sailor Moon:
  • Sailor Galaxia is the Big Bad of the fifth and final arc, but the one who drove her actions was the Death Phantom, the Big Bad of the second arc.
  • Chaos. All the main antagonists, except Sailor Galaxia, were agents of his (albeit unknowningly). So basically Chaos is the main instigator of all the events of the manga. Also, while Galaxia isn't an Unwitting Pawn of Chaos like the previous main villains, she's actually The Starscream of Chaos and joined him willingly. This, and the fact that Chaos was the aforementioned Death Phantom, means that Chaos also hijacked the last arc anyway.
• Gordon attempts this in the finale of Scott Pilgrim Takes Off, aiming to blow up the theater in which it takes place and reclaim his power, but it's subverted. Even Older Scott utterly bodies him, and it's only Matthew Patel's pity and disinterest in running a multibillion-dollar empire that give him everything back in the end. He and Julie do get to be in the Sequel Hook, though.
• The Phantom Bullet arc of Sword Art Online has the heroes fighting Death Gun, a virtual Serial Killer. It’s eventually revealed that the Death Gun avatar is controlled by ex-Laughing Coffin member XaXa, a.k.a. Shouichi Shinkawa.
• Symphogear seems to like subverting this trope:
  • The second season implies that Fine will be the ultimate Big Bad again, but when she finally appears, she immediately does a Heroic Sacrifice for the good guys.
  • GX has Dr. Ver reappear suddenly, but the current Big Bad quickly betrays him, so he also ends up pulling a Heel–Face Turn and Heroic Sacrifice. (Fine apparently reappears in GX and has returned to team evil, but she doesn't last very long or overshadow the current Big Bad.)
• In Violence Jack, which takes place in the Devilman universe, it is eventually revealed that the Slum King is Demon Lord Zenon, who along with the whole world was recreated by Ryo Asuka aka Satan. They both become the dual Final Boss. Also inverted in that the titular protagonist turns out to be a reincarnated Akira Fudo.
• In Yatterman Night, a sequel series to the original Yatterman, the Big Bad is Lord Yatterman, the leader of the New Yattermen who took over after the death of Dokurobey, the villain of the original series and leader of the Doronbo Gang. Lord Yatterman is a Knight Templar who imposes a brutal dictatorship on the people and fights against the new Doronbo Gang to prevent another rise of evil. Until Episode 10 reveals that “Lord Yatterman” is Dokurobey himself, having survived and taken over the Yattermen with the intention of turning them into a brutal dictatorship, destroying their reputation in the process, as revenge for all his past defeats.
• In Yu-Gi-Oh! The Dark Side of Dimensions, Aigami/Diva is the Big Bad, but for the finale he's corrupted by a familiar source - the Millennium Ring, capable of corrupting the holder even after Zorc was purged from it.

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