Hijacked By Ganon / Western Animation

• More than one Adventure Time plot has turned out to have the Ice King behind it, occasionally nonsensically. This was likely parodied in the Season 2 finale, where all he did for the first part was hang around annoying everyone and trying to be involved in the story, even though there was a bigger villain around.
• The Adventure Time: Distant Lands episode "Together Again" introduces a new antagonist, New Death, who wants to destroy all the realms of the afterlife and stop the cycle of reincarnation. Only at the end does it turn out he was being manipulated by the Lich the whole time, who continues his pursuit of killing everyone in existence, even after death. It's a fitting sendoff because the episode is the Grand Finale of the entire series and Finn and Jake are facing off against the effective Big Bad of the story once again, even at the very end.
• The Season 3 finale of Archer, "Space Race", has Archer and the ISIS crew board a space station to stop a mutiny, only to get caught in the station commander's plan to colonize Mars. Once he commits suicide, it seems for the moment they only have to worry about getting back planetside — until Barry, Archer's cyborg rival who is hellbent on killing him (long story), just happens to show up (having known he'd be there thanks to Krieger).
• The Ba Sing Se arc of Avatar: The Last Airbender played up Long Feng as the storyline's Big Bad. But then Princess Azula came along and took center stage. Long Feng, on his part, actually saw this trope coming and attempted to betray her, but unfortunately for him, Azula managed to turn his own soldiers against him.
• The Legend of Korra: It's revealed in "The Stakeout" that Zaheer and his gang are part of a group called the Red Lotus, which Unalaq (The Heavy in Book 2) was initially part of.
• Season 3 of Ben 10 introduced in one episode a werewolf-like alien who was seemingly killed at the end of his episode, but was revealed to have built a machine as a Sequel Hook. A mummy-like alien is then introduced in a later episode. Both come back and are revealed to work for a new villain named Dr. Vicktor in the first part of the season finale...and then it turns out Dr. Vicktor himself was The Dragon to Ghostfreak/Zs'kayr, a villain who had been introduced in a previous season 2 episode.
• Both seasons of Ben 10: Ultimate Alien used this trope:
  • Season 1 featured Magnificent Bastard Aggregor as the main antagonist, whose scheme remained unstoppable for most of the season...then, when it was about to succeed, Kevin sacrificed his sanity by using the part of his power that would cause him to go crazy again to stop him. After he is defeated, Kevin, now back to being a psycho, serves as the main villain for the remaining episodes of the season.
  • Season 2 is even more complex; it starts with a Big Bad Ensemble involving a war between the Forever Knights and a new, mysterious sect that turns out to be manipulated by Ben's Arch-Enemy Vilgax. Then an Eldritch Abomination Vilgax had been impersonating shows up and takes Vilgax as his Dragon, apparently becoming the new Big Bad...until Vilgax betrays him, absorbs him and becomes the final villain of the season.
  • Ben 10: Omniverse has an In-Universe example. In the first 10-episode arc, Khyber the Huntsman is the Big Bad. In the 2-part finale however, it's eventually revealed he actually is working for Dr. Psychobos, an Evil Genius Cerebrocrustacean who invented Khyber's main weapon, the Nemetrix with the aid of Malware, a Predecessor Villain who was introduced in this series, but whose first appearance chronologically happened between the original series and Alien Force, and who had only been seen in flashback at this point.
• Buzz Lightyear of Star Command has Evil Emperor Zurg, who is responsible for practically every other threat Team Lightyear goes up against. Buzz is very much aware of this.
• In the Captain N: The Game Master episode "Quest for the Potion of Power," Mother Brain uses the titular potion to revive Ganon so she can control him.^note Only the original NES games existed at the time of the cartoon, so Mother Brain was essentially hijacking the plot of Zelda II: The Adventure of Link. Three guesses how that went.
• In Gargoyles, for a large chunk midway through the series a group of three god-like beings called the Weird Sisters pop up from time to time, manipulating the main cast for their own ends. It turns out in the epic three-part episode "Avalon" that they were answering to the Archmage, a previous villain who was believed to be dead, and all their plotting had been to help him conquer the titular island (or at least that's what they told him they were doing...) It would probably be better to say they were Dragons With An Agenda. The trope still stands, however.
• Hurricanes: In "Escape to Freedom", the Hurricanes were captured by a soccer-obsessed General of a Banana Republic and forced to play against his soccer team. It was revealed to the viewers but not to the Hurricanes (albeit it's implied the team's owner suspects) Stavros Garkos made an agreement to keep them from showing up for an upcoming game so Garkos' own team, the Garkos Gorgons, would win by default.
• Season 3 of Jackie Chan Adventures has the Season's Big Bad, Daolon Wong, resurrecting Shendu in order to obtain the wayward Dragon Talisman power. The results are obvious.
• In Justice League
  • It's revealed that Lex Luthor was being manipulated by Brainiac to build him a new body. Luthor had been infected by a copy of Brainiac's programming after Brainiac had exploded the last time he and Luthor had met.
  • More to the point, Luthor and Brainiac take over the Big Bad post from Cadmus by showing Luthor had manipulated Cadmus, gaining access to their technology so he could build a new AMAZO and upload his mind (or, rather, Brainiac's mind) into it. The writing staff admitted on the DVD commentary that they had no idea how to make the plot of season 2 untangle on its own due to the Grey-and-Gray Morality situation that had arisen, so they went with an "old reliable" and let a Black-and-White Morality villain take over so they could have a proper fight finale.
  • In the subsequent story arc, this happens twice. Gorilla Grodd's leadership of the Legion of Doom is usurped by Luthor, then Lex's plan to reassemble Brainiac is throttled when he accidentally brings back Darkseid instead.
• In Legion of Super Heroes (2006), Imperiex, season 2's Big Bad, teams up with Brainiac 5 (Who had been taken over by the programming of Brainiac 1.0). Just as Imperiex broadcasts their alliance to the Legion, Brainiac 5 impales and disintegrates Imperiex, then takes control of Imperiex's forces himself.
• My Little Pony: Friendship Is Magic:
  • Double Subverted. When vines from the Everfree Forest started invading Ponyville and the princesses went missing in the episode "Princess Twilight Sparkle", everyone assumed it was a new threat or villain causing all this. In Part Two it seems to be because of Luna becoming Nightmare Moon again, when it's revealed that it was all a flashback. Then it gets double subverted at the end. It turned out that it was caused by seeds that the recently reformed villain Discord planted right before his defeat by Celestia and Luna over a millennium before. The Tree of Harmony's power managed to keep them from growing for that long.
  • A literal variation happens in the series finale. Throughout the ninth season, it looked like it was buiding towards Grogar being the Final Boss of the series, with him bringing together Equestria's remaining unreformed villains into a Legion of Doom and having them under his hoof. It turns out, however, that it was actually Discord in disguise, though he did so with good intentions, planning to use the villains to give Twilight some easy victories to boost her confidence as the new ruler of Equestria. Unfortunately, the villains managed to outsmart him, double-crossed him, and used the Bewitching Bell to remove his magic so he couldn't keep them in line, leaving them to be the true final threat of the series.
• The Owl House sets up the Big Bad of the third season to be The Collector, released from their prison as a result of the heroes risking Summon Bigger Fish as a last ditch solution to the previous villain Emperor Belos. The final episode sees the heroes help the Collector undergo a Heel–Face Turn while Belos becomes the final threat of the series when he seizes control of the Titan's heart and uses it in a final attempt to destroy the Boiling Isles.
• In the second season of W.I.T.C.H., the first season's Big Bad, Phobos, escapes in one episode and takes over a team of recurring vilains, the Knights of Vengeance, from Nerissa. Justified in that they were Remnants of his army and still loyal to him and that Nerissa didn't need them anymore anyway. He was quickly defeated by Eylon and Nerissa reclaimed her position of Big Bad by tricking Eylon into giving up her powers. After Nerissa later acquired the powers of the Heart of Dumbala, the girls grew desperate and decided to ally themselves with Phobos as only a member of the Meridian royal family was capable of forcibly taking the Heart of Meridian. This, of course, ended with him stealing Nerissa's powers, reclaiming his army and throne while setting his sights on multiversal conquest. At least until Cedric pulled a Starscream and stole his powers.

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