Hijacked by Ganon



"You're just now figuring out where Zant got his power?"

- Midna, The Legend of Zelda: Twilight Princess

An inverted form of The Man Behind the Man. Rather than a new evil being behind an old villain, an old villain is behind a new one.

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

Can sometimes be a form of Giant Space Flea From Nowhere, except that the 'flea' in this case is at least known as a major part of the setting, even if they haven't had any apparent role in the plot of a specific installment so far. Usually not to be confused with Hijacked by Jesus, though theoretically something Hijacked by Ganon can become Hijacked by Jesus. A subversion of Outside Context Villain, in that the Outside Context Villain is actually subordinate to a villain who is not outside context.

Keep in mind that this is about plot twists, so EXPECT SPOILERS!

The Legend Of Zelda (Ganon/Ganondorf)
Several times in The Legend of Zelda series the hot new Big Bad turns out to simply be a pawn of Ganon.
 * In the Oracle games,
 * Four Swords Adventures is a odd mixture of this and The Man Behind the Man. Vaati is a reoccurring villain from the prequel game, and is further established in an earlier prequel, but about halfway into the game we find out that Ganon is the true villain of the story, just using Vaati as a decoy. In this case, Ganon hijacks the game from the newer villain Vaati, but Vaati was already an established villain as an alternate to Ganon, so Ganon becomes The Man Behind the Man as well.
 * Then there was Zant of Twilight Princess, who, after being built up as "The Twilight King", became the victim of yet another twist hijack by Ganon. While this caused a lot of debate, it was already known before the game came out that Ganon was going to be in the plot and Zant does allude to Ganon being behind him the first time you encounter him.
 * Subverted in Link's Awakening where Ganon appears during the final boss battle, but it is only a form taken by the Nightmare based on Link's memories.
 * Played with in Skyward Sword, as

Anime and Manga

 * Hijacked by the Sharingan is what many fans think Naruto has become ever since
 * Vamdemon/Myotismon in Digimon Adventure 02.
 * 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.
 * A key plot element in Umineko no Naku Koro ni, also Most of End of the Golden Witch involves  and  doing the hijacking.
 * In Zatch Bell, Riou serves as the main villain for the Faudo arc -- . And it happens right after, too.
 * 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.
 * The Heaven's Lost Property manga
 * Puella Magi Madoka Magica's Spin-Off Puella Magi Kazumi Magica.

Comic Books

 * Norman Osborn's revival at the end of The Clone Saga definitely counts. We in the real world know he was brought in because the story had long since gotten out of hand, and the best way to resolve it neatly was to have one mastermind behind everything. Osborn, a notorious Chessmaster, was judged the only Spidey villain with the oomph to pull it off (even if they had to bring him back from the dead).
 * In Ultimate Marvel, Dr. Doom has pulled this three times to date: in . Which is weird, because he doesn't have nearly as much cred as his 616 counterpart, and except for those two instances, no one besides the Fantastic Four has dealt with him...but there you have it. The former kind of worked, the latter...not so much.
 * A flaw in the later seasons of the Elf Quest series is that the main villainess Winnowill turns out to be the one behind the machinations for every single plot. Shards? Yeah, that was her, shapeshifted. Wavedancers? Yup, her again. Forevergreen? Oh look, it was her insane minion. Hidden Years? Guess who made all those mutant monsters? It gets old.
 * The bizarre, surreal and hilarious—as with everything else in the book—reveal of the Comte de Rochefort as the Man Behind the Man in Jason's The Last Musketeer.
 * Rastapopoulos makes a few surprise return appearances as the Big Bad in a few Tintin albums (although not as many as fans seem to think).
 * In the Sin City tale Hell And Back,
 * Taken Up to Eleven in Amazons Attack. A brainwashed Queen Hippolyta has led the Amazons of Themyscira to wage war on the United States! BUT WAIT! It turns out that Queen Hippolyta's attack was actually all a Secret Test of Character by the goddess Athena! BUT WAIT! It turns out it was all a convoluted plot masterminded by Granny Goodness of the New Gods while disguised as Athena and keeping the other Greek gods imprisoned! BUT WAIT! The entire miniseries was actually a tie-in to Countdown to Final Crisis, where Granny Goodness is training hundreds of women to be female furies in connection to the Death of the New Gods! BUT WAIT! The Death Of The New Gods/Jimmy Olsen's superpowers plotline from Countdown was actually all part of Darkseid's evil plan involving the Anti-Life equation, and Granny Goodness was just working for him! WHAT.
 * The finale of the Darkwing Duck comic, "Dangerous Currency" has Magica DeSpell and the Phantom Blot using a corruptive inky substance (which brings Epic Mickey to mind), only for the substance to be Negaduck after a Literal Split Personality experience that transformed him into a Gray Goo. He regains physical form, hijacks the story and takes the Blot's offer of an Assimilation Plot that merges the other villains into Negaduck.
 * European Donald Duck and Mickey Mouse comics did a story arc about an evil wizard who brainwashed Beagle Boys, Magica and Phantom Blot to serve him and keep the protagonists busy while he will carry on his evil plan. Phantom Blot however turned out to be just pretending to be brainwashed so he could stike at him and take over his scheme. In the end it was subverted, because the wizard ran away right after that, keeping his status of the Big Bad for the final part of the story.

Film

 * Palpatine coming back in The Rise of Skywalker is this, since the Star Wars Sequel Trilogy already has a perfectly good conflict between the Rebellion and the First Order. In this case, Palpatine turns out to be the hidden mastermind behind the First Order, and is the apparent creator of Supreme Leader Snoke. It does not help that his being the hidden behind the scenes villain was not foreshadowed in any way during the previous two films.

Literature

 * In Artemis Fowl: The Time Paradox, the apparent villain-of-the-day (or yesterday) Damon Kronski turns out to be the pawn of.
 * The original novel of You Only Live Twice. So James Bond needs to get his mojo back after Blofeld got away and murdered his wife out of spite last time. Well, through a complicated series of events, Japan tosses him a relatively easy one: Some loon named Doctor Shatterhand is running a poisonous garden and encouraging suicide. Investigating that should jump-start him out of his funk...dum-da-da-da! It's Blofeld again! And he's crazy!
 * Harry Potter and The Chamber of Secrets plays out like this. So a monster controlled by the Heir of Slytherin has been attacking students. At the end, we discover that -surprise!- Voldemort was behind the entire thing.
 * Averted in Harry Potter and The Prisoner of Azkaban. It is the only book where Voldemort isn't the Big Bad.
 * A Series of Unfortunate Events plays with this: about half the books introduce a new character that turns out to be Count Olaf in disguise; however, the Baudelaires see through it early on and spend the rest of the book trying to convince the bumbling adults in charge.
 * Also used for Olaf's many minions, at least one of whom always accompanies him in his schemes. Weirdly, the children never really are able to recognize them until the very end, despite the fact that the children are usually told that said minions just showed up in the area recently and they quickly notice suspicious characteristics about them. . It's not until the end of the book that the identities are revealed, which leads to the siblings inevitably trusting the newly-captured Olaf into the hands of the kind, innocent doctor or police officer that they just met.
 * Substitute Ganon with Takhisis and you have the entire War of Souls trilogy in the Dragonlance series.
 * Books Of Bayern: In the fourth book, shows up again after having supposedly been executed at the end of the first book...and as if that wasn't enough, the same character claims to have been indirectly responsible for the events of books 2 and 3 as well.
 * Warrior Cats: Sol is probably the only villain in the entire series that isn't somehow connected to Tigerstar.
 * Probably? He IS the only villain not connected to Tigerstar—they could've named the trope after him.
 * Honor Harrington: The genetic-slavers (and Designer Babies) of Mesa and Manpower Inc have basically been puppeteering the Star Empire of Manticore and the People's Republic of Haven since near enough the beginning of the series. Their plans are almost Palpatine-esque in their intricacy.
 * Kitty Takes a Holiday is an interesting example in that "Ganon" is a
 * In the Vorkosigan Saga, The Vor Game is a good example. The entire plot is Hijacked by Cetaganda.
 * In-universe example—the main threat for most of Malazan Book of the Fallen is the Crippled God, but in the last few books, his power is usurped . While hadn't previously appeared as villains in the books themselves, they were a threat from the world's prehistory, so many of the characters, particularly the immortals, see it as this trope.
 * At least from the perspective of the majority of the world, this is what does to the Anti Christ in the Left Behind series.
 * In the first three Black Company books, Dominator is a well-known Bigger Bad to Lady's Big Bad, so when he, it's this trope in-universe.
 * Subverted later in the series with new Big Bad  Longshadow. It's heavily hinted he's someone the protagonists have faced before, supported by one of his minions turning out to be a previous antagonist and his own habit of going around in a mask and cloak that completely conceals his appearance. When they finally capture him, however, he turns out to be a complete stranger whose history is entirely unconnected to the previous books.
 * Pick any Sherlock Holmes story, and you'll find a scholar who holds that Moriarty was behind it. Of course, the opening of "The Adventure of the Norwood Builder" more or less declares open season on this behavior, but that still doesn't account for such theories for stories that take place after Moriarty is supposed to have died.

Live-Action TV

 * One loses track of how many Doctor Who serials open with a seemingly original villain who turns out to be a pawn of the Daleks, the Cybermen, the Sontarans, or the Master. Or sometimes more than one of them (and sometimes they hijack each other). The production team would later admit that they overdid it in the eighth series (which introduced the Master), making him the primary villain in all five serials.
 * On one occasion, The Master was the pawn of the Daleks (incidentally, that was Roger Delgado's last appearance as the character), who were only revealed at the very end as the men (well, hideously mutated squidlike ex-Kaleds in bonded polycarbon armor) behind the man.
 * In the new series, it turns out the Daleks were leading the Mighty Jagrafess into manipulating the Human Empire's population. Subsequently, they were behind the Gamestation's gathering of humans for their deadly game shows.
 * Then the Cybermen hijacked Torchwood, the Master hijacked Harold Saxon (by being him), and the Cybermen, Daleks, Sontarans, and a few others hijacked the Pandorica. Yup, still going strong.
 * In Star Trek: Deep Space Nine, the revelation that the Breen were working for the Dominion was done in a similar fashion.
 * More obvious was in the Star Trek: The Next Generation episode "Descent", when the rogue Borg the Enterprise has been chasing turned out to be led by Lore.
 * The majority of new villains introduced on Days of Our Lives in the past 15 years have been revealed to be working for Stefano Di Mera.
 * The Grenada adaptation of the Sherlock Holmes mystery "The Red-Headed League" ultimately connects its mastermind with Holmes' archnemesis Moriarty. No such connection exists in the original story.
 * However, the real-life crime that inspired "The Red-Headed League" was masterminded by the man who inspired Moriarty, sooooo...
 * The second, third, and fourth volumes of Heroes have been hijacked by Sylar, who, while not the mastermind of the first volume, was the unwitting means to Linderman's end, and much more deadly. The volumes set up their Big Bad as, in order,, only for them to be dealt with a couple episodes before the end of the volume, generally unceremoniously. Sylar's MO is to pop out of nowhere at around that time and catch everyone with their pants down, brewing some mayhem for an episode or two until the heroes get him under control...at least until the next volume begins.
 * This is made all the more predictable by each volume's insistence on having a major plot thread centering around Sylar regaining his powers, deciding he'd rather be evil, or remembering who he is.
 * In one episode of The Twilight Zone, a neo-Nazi campaign is hijacked by a mysterious phantom who delivers excellent advice on public speaking. It turns out that the phantom is none other than
 * Buffy the Vampire Slayer, it turns the source of various nasty events happening around and to her circle of friends, not to mention the forces of good around the world, are the work of The First, who appeared in Season 3 as a Monster of the Week and is now the final villain of the show.
 * And then in the Season Eight comics, it turns out Twilight is actually.
 * 3rd Rock from the Sun gives a humorous example. Dick is outraged when he discovers Mary has been getting love letters from a mysterious admirer, and discovers that it's actually his Arch Enemy Liam, who seduced Mary and tried to destroy Earth once before and is back to give both another shot.
 * In Lost,
 * In the final season of 24,
 * Also, in The Game,
 * Subverted in season six;
 * Whenever Kamen Rider pulls off a Massive Multiplayer Crossover, you can be sure that the series' original Nebulous Evil Organization, Shocker, would have its name all over the plot.
 * And in the old days, Shocker's Great Leader turned out to be behind any number of evil organizations.
 * In Tokusou Sentai Dekaranger vs. Bakuryuu Sentai Abaranger, the villain's plot was revealed to be to resurrect not only all the Alienizers and Trinoids that have been slain in battle, but Dezumozorlya (the Abarangers' Eldritch Abomination Big Bad) as well. Fortunately, It is played straight, however, in Engine Sentai Go-onger vs. Juken Sentai Gekiranger,
 * In the tokusatsu series Ultraman Nexus, there is a constant reference of "The Unknown Hand" being the mastermind behind everyone of the Space Beasts actions, as well as reoccurring baddie, Dark Mephisto.

Professional Wrestling

 * In 1999, WWE featured a long and convoluted storyline about The Undertaker and his Ministry of Darkness attempting to seize control of the WWE from former bad guy Vince McMahon under the orders of a mysterious figure known only as "The Higher Power". This "Higher Power" turned out to be...Vince McMahon. The Ministry of Darkness then merged with The Corporation to become the Corporate Ministry, and about five months of storyline were thrown out the window.
 * In WCW, there was the infamous Sting vs. the Black Scorpion angle. In August 1990, after wrapping up another chapter in his on-again/off-again feud with Ric Flair, Sting started being harassed by a mysterious masked man who spoke with a heavily altered voice. The standard "masked wrestler" plotline quickly got out of control, incorporating bizarre promos, "messengers" that attacked Sting at house shows, and ringside stage illusions. After four months of this nonsense, the Black Scorpion was finally revealed to be...Ric Flair. Behind the scenes, this was an Author's Saving Throw- WCW constantly alluded to the Black Scorpion actually being The Ultimate Warrior in an attempt to get Warrior to jump ship from WWF. When it didn't work, they shoehorned Flair in instead. Wrestlecrap has a detailed write-up of the debacle.
 * Another WWE mystery: "Who ran over Stone Cold Steve Austin?" Well, the man driving the car was revealed to be Rikishi, whose lame Motive Rant killed any potential heat. Rikishi was so ill-fit for the Heel role that after one month the much better established Triple H was revealed to be The Man Behind the Man.
 * In reality, the mastermind couldn't have been anyone BUT Triple H. Triple H assaults Austin backstage, runs off, lures Austin out into the parking lot, where Rikishi just randomly happens to be in a car in the parking lot ready to run him over. Despite Triple H's insistence right before Rikishi's reveal that he was planning to lead to Austin to a beatdown, the variables are just too unlikely for it to be anybody but Triple H.
 * The Nexus was a group of scorned rookies out for revenge against the mainframe of the WWE...only for them to eventually becomes lackeys of the already well-established CM Punk.

Tabletop Games

 * The Legend of the Five Rings Gold Edition story arc introduced Daigotsu, the mysterious new lord of the Shadowlands. Daigotsu was able to dispatch the venerable powerhouse characters Toturi and Kyoso no Oni with ease and brought with him never-before-seen monsters such as the Tsuno and Onisu. He even managed to level Rokugan's capital city of Otosan Uchi...at which point he released Fu Leng, the setting's de facto Big Bad from the realm of the dead and who then took on the role of the arc's Final Boss. Interestingly, Daigotsu played an indirect role in Fu Leng's defeat thanks to Hantei Naseru running a successful Batman Gambit on the latter regarding the former's loyalty.

Toys

 * Teridax, the main Makuta from Bionicle got into the habit of this. The first two years after Teridax was first defeated, it was known he orchestrated the new antagonists to fight the heroes, but the two year after that it was part of The Reveal, the year after that not so much but did involve his cronies setting him free, then after that it was again revealed he had basically been behind it all. The next year Teridax was a major player, and then the last year was the culmination of his master plan to take over the universe.

Video Games (Excluding Ganon)

 * in Sonic Rush Series Adventure.
 * Also in Sonic Heroes.
 * in Sonic Generations.
 * This is Dr. Wily's trademark tactic in the Mega Man series. He pretended to reform in Mega Man 3, and in all subsequent main series games except Mega Man 7 and Mega Man 8, he turns out to be using the initial villain or some other phenomenon as a decoy. The reason he doesn't in Mega Man 7 is that the game begins with Wily being arrested, but his robots activate themselves and free him. Also does it in V for the Game Boy with the Star Droids. Amusingly, the game doesn't even try to hide that he's the final boss of Mega Man 9 or Mega Man 10, as the achievement for beating each game is named "Whomp Wily!".
 * In the Mega Man X games, Sigma hijacks all the main villains from X2 onwards, to the point it's a twist that he isn't the Big Bad of X8. It gets Lampshaded in X4 when Split Mushroom responds to a demand to reveal the mastermind behind the game's plot with his meme-tastic Catch Phrase "Take a wild guess", after which his lifebar appears, blatantly carrying Sigma's logo, unlike previous bosses.
 * And then 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. And because of his hand in the creation of the virus and Zero, he 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.
 * In the Mega Man Battle Network games, 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, . However, the villain of 4 and 5 is the organization Nebula, lead by Wily's son.
 * Andross also pulled this one in Star Fox Adventures. You even have to beat him the same way as in 64.
 * Kingdom Hearts, thanks to its confusing cosmology, has a rather weird example: the Big Bad of the entire series is Xehanort, who is technically "dead" but acts as the antagonists of most of the games through his Heartless "Ansem" and his Nobody Xemnas. Ansem was The Man Behind the Man to the Disney villains, and Xemnas' connection to Ansem was a twist to KHII. In Birth By Sleep, we find out that, and then Dream Drop Distance has its primary villain turn out to be . As a result of that, almost every single villain in the series can be traced back to Xehanort directly or indirectly, and his connection to the main villain of the latest game is always played as The Reveal. If the promised Kingdom Hearts III is as straightforward with who its villains are as Dream Drop Distance foreshadowed, it'll be a first.
 * There are two semi-exceptions: The villains of Chain of Memories are, and the closest Kingdom Hearts coded gets to a true villain is.
 * Bowser in Super Mario Sunshine. It turns out
 * It's kind of a twist in Mario & Luigi: Superstar Saga. The primary villainess throughout the plot is Cackletta. However, So while the final dungeon and boss starts out very Bowserlike, especially with the return of, it eventually boils down to you vs. "Bowletta".
 * Bowser also does a hijacking in the original Yoshi's Island. You enter the final area and confront Kamek, the essential main antagonist...who is then stomped on by Baby Bowser. Cue obligatory final battle.
 * Averted, but attempted in Paper Mario: The Thousand-Year Door, where Bowser is not the main antagonist. He and Kammy Koopa appear in several cut scenes 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 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.
 * Because seriously, "What's a finale without a Bowser appearance, huh? A cruddy finale, that's what!"
 * Played with in Super Paper Mario. The heroes go to his castle without even checking if he is the bad guy this time. He was not.
 * Super Mario RPG did this in reverse—the game opens with Bowser kidnapping the Princess, again, and Mario rescuing her, again. He complains about how annoying this is. At which point the real villain shatters the Star Road and ejects Bowser from his castle. Bowser joins your party later in the game to serve his own purposes, and he remains firmly against Smithy for the entire game.
 * Super Mario Bros 3 uses a variation of this: you know from the beginning of the game that Bowser was responsible for transforming the kings of the Mushroom World into animals, but it isn't until you reach World 8 that you find out that
 * In Mario & Luigi: Partners In Time, Baby Bowser is a recurring nuisance, and Bowser only shows up late in the game to kidnap the princess and fight the brothers once. At the end of the game, however, after the brothers defeat Princess Shroob,.
 * Mario & Luigi: Bowser's Inside Story takes an interesting spin on this. You'd think that, Bowser being one of the protagonists, he wouldn't be able to hijack the plot.
 * Luigi's Mansion
 * Then it gets confusing to say if it happened or not, because
 * And then there's the Epileptic Tree that
 * Dance Dance Revolution: Mario Mix was guilty of this too. 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. You can imagine that the former's fans were not amused.
 * 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 General. The fifth game, Defiance, revealed that Hash'ak'gik and the Hylden General were the same being all along..
 * 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 for unknown reasons (it's unclear whether he did it on his own, or for ).
 * 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;
 * 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.
 * Subverted in Aria of Sorrow with
 * In Dawn of Sorrow,
 * Not quite.
 * 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 (Nintendo 64):
 * In both Curse of Darkness and Order of Ecclesia, Dracula yet again comes out of nowhere at endgame.
 * 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,
 * To some extent, the entire plot of Castlevania Judgment is preventing Dracula from being Hijacked By Galamoth (of Kid Dracula and SotN fame).
 * Subverted as hard as possible in Lords of Shadow.
 * King K. Rool (or, as he preferred to be called in this game, Baron K. Roolenstein) in Donkey Kong Country 3: Dixie'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.
 * Averted in Donkey Kong Country Returns. really is the final boss of the game.
 * Fallout, while not actually a character, the Forced Evolutionary Virus, a mutagenic serum used by the first game's Big Bad, was brought back in the end stages of the second game as part of the new villain's plan to wipe out the wasteland. The villain of the third game was essentially repeating his plan but with a few tweaks.
 * In City of Heroes, it's all a Nemesis plot; he 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 Cimerora zone was only introduced after the appearance of Ouroboros.
 * True veterans of the game know it's only a matter of the time until the writers make Nemesis responsible for 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 pulling the strings.
 * 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 . Talk about having it in for your son...
 * In System Shock 2, you initially believe that Xerxes is the Big Bad causing havok on the Von Braun.
 * In BioShock the first part of the game focuses on you hunting down and killing Andrew Ryan, only to learn.
 * Little Big Adventure 2: Twinsen's Odyssey. Turns out the aliens are just dupes of good ol' Doctor Funfrock.
 * The Bubble Bobble Spin-Off Bust-A-Move, AKA Puzzle Bobble: In the VS CPU modes of installments 2 through 4, a 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.
 * 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.
 * 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.
 * Outright inverted by Dedede from the Kirby series. He was the Big Bad and Final Boss of the Original Kirby's Dreamland. In all subsequent games he is demoted to Disc One Final Boss, and by Squeak Squad, Kirby pretty much beats him up for shits and giggles as soon as his cake is stolen. He even outright helps Kirby in Kirby 64.
 * 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 latest story arc (The NESTS Chronicles), 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.
 * In several Metal Slug games, Morden's evil scheme for domination is hijacked right at the end by Martians. In another iteration, the Martian's plot is hijacked by martian eating, Giant Space Flea From Nowhere race of aliens.
 * Ninja Gaiden II on the NES spends a lot of time building up Ashtar, the self-proclaimed "Emperor of Darkness," as the Big Bad. The opening cinematic goes so far as to suggest he was the Man Behind the Man in the previous game. 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, and the Man Behind the Man who was behind Ashtar.
 * 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.
 * 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,.
 * 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 Just to drive the point home, the final scene has Carmelita destroy a vital component that renders Clockwerk Deader Than Dead.
 * In Ratchet and 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
 * In Jak 3, it's revealed that
 * The True Final Boss of World of Warcraft's Burning Crusade expansion is Kil'jaeden the Deceiver, one of the arch-demon lords of the Burning Legion and the mover behind most of the events of the expansion. However, his appearance in the final content patch came as a surprise to almost everyone, since all of the promotion for BC was focused on the confrontation with Illidan. Even the mighty Kael'thas Sunstrider was seen as something of a throwaway boss—a stepping stone to Illidan—until it was revealed that he was acting as The Renfield for Kil'jaeden.
 * Kil'jaeden and Archimonde were also behind most of the events of the RTS Warcraft games. Horde invasion? That was them. The Scourge? Yep. Illidan? Kil'jaeden again.
 * The Burning Legion does have local competition in the form of the Old Gods, who control two of the four elemental lords, the Qiraji, living Nerubians, the Watchers of Ulduar, the Twilight's Hammer cult, Cataclysm's Big Bad Deathwing and yet-to-be-seen Queen Azshara.
 * In Endless Frontier, there's a whole lot of new characters and villains, but  are the real enemies.
 * In the first four Phantasy Star games, the Big Bad revealed early on might be an evil king, an evil intelligent computer, a scorned and now vengeful half-human monster, a fabricated war between the heroes' civilizations, or an omnicidal Evil Sorcerer, but they're all revealed to be pawns of Dark Force. In the fourth game,
 * When they say that darkness cannot be killed, they aren't kidding. Phantasy Star Online? Dark Falz. Episode II? Dark Falz' corruption. Episode III? Dark Falz fragments. Move on to Phantasy Star Universe, and what's the source of the SEED ? Dark Falkis. Episode II, III and Portable all have Illuminus essentially side-by-side with Dark Falz. Averted with Portable 2, then ultimately Played Straight with Portable 2 Infinity and the 108 fragments of Dark Falz.
 * In Metroid: Other M, the events aboard the BOTTLE SHIP are the fault of.
 * With no real buildup, Carnage randomly appears as the final boss of Venom/Spider-Man: Separation Anxiety.
 * Zig-zags 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 that character to have been dead since the first two games, so it's a shock to them when his identity is revealed. He laughs.
 * 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, and the roc feather quest takes a backseat to stopping the Grave Eclipse.
 * 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 assult on the sub-sector Aurelia was orchestrated by.
 * 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.
 * 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.
 * Even though everyone pretty much shrugged and said "It's probably Reapers" in the first conversation about the Collectors.
 * In Persona 3: The Answer: After destroying the mysterious shadow that you've spent 90% of the game chasing, a new, unconnected Big Bad takes over:
 * Valkyrie Profile: Silmeria is hijacked at the end by
 * 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.
 * 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 . Then, get ready for this, Oh, and  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.
 * Yakuza 5 has suddenly return as Kiryu's final boss. It comes with a Lampshade Hanging, as his reply to Kiryu asking what he's doing here is "I'm not really sure myself".
 * Yakuza 5 has suddenly return as Kiryu's final boss. It comes with a Lampshade Hanging, as his reply to Kiryu asking what he's doing here is "I'm not really sure myself".

Web Comics

 * In Sluggy Freelance,.
 * Not to mention several dangerous situations set up by.
 * And then there's HeretiCorp, which at least usually has its logo on everything, except during its man-behind-the-man-who-was-actually-behind-the-first-man-anyway plots. Really, it's getting less "Is this _____ or a new enemy?" and more "Is this ____ or ____?"
 * In Adventurers!, Khrima was the first villain, only to later be hijacked by Eternion. This is parodied, like everything else in Adventurers!, when Khrima and Eternion have an election campaign on who gets to be the Final Boss. Eternion got his boss fight, but Khrima afterward comes from out of nowhere with a Very Definitely Final Dungeon and the Final Boss fight.
 * The "Army Of One" storyline in The Adventures of Dr. McNinja, where the antagonist(s) seem to be a bunch of sky pirates who have kidnapped a clone of Doc, but the whole thing is really a plot by

Web Original

 * In Chaos Fighters II-Chemical Siege, after the true villain is revealed as, when Enrei and Gareia finished him, it was revealed that , the Big Bad of Cyberion Strike, did everything, including.
 * In Arby 'n' the Chief,

Western Animation

 * 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.
 * In Justice League Unlimited, it's revealed that.
 * More to the point, 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 an Black and White Morality villain take over so they could have a proper fight finale.
 * And in the subsequent story arc, this happens twice..
 * Season 3 of Jackie Chan Adventures has the Season's Big Bad, Daolon Wong, . The results are obvious.
 * Season 2 of Avatar: The Last Airbender played up Long Feng as the Season's Big Bad. But then Azula came along and took center stage. Long Feng on his part was Genre Savvy enough to actually see this trope coming and attempted to betray her, but unfortunately for him Azula managed to turn his own soldiers against him.
 * 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.
 * In second season of WITCH first season's Big Bad, Phobos, escapes in one episode and takes over team of recurring vilains, Knights of Vengeance, from this season's Big Bad, 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 position of Big Bad by tricking her into giving up her powers. After Nerissa later aquired powers of another dimensional Heart, girls grew desperate and decided to ally themselves with Phobos who is the only person in The Multiverse capable of taking powers of the Heart against the owner's will. Which of course ended with him stealing Nerissa's powers, taking over his army and deciding to start multiversal conquest..
 * Season 3 of Ben 10 introduced in one episode an werewolf-like alien who was seemingly killed at the end of his episode, but was revealed to have built a machine as a Sequel Hook. A mummy-like alien is then introduced in a later episode. Both come back 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.
 * Season 2 of Ben 10: Ultimate Alien does it again by starting with a Big Bad Ensemble involving a war between the Forever Knight 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 shew up and took Vilgax as his Dragon, apparently becoming the Big Bad... until Vilgax betrays him, absorbs him and becomes the final villain of the season.