Prologue: Hey! Did you know that in the last game there was this nutty computer that tried to kill everyone? Yahtzee: No, I did not know that. Why did you bring it up? Prologue:Errrmmm, no reason. Here's a totally unrelated plot. Also try not to look at the box art.
A Link to the Past features an odd, ambiguous situation due to the fact that main villain Agahnim is said, depending on version, to be either a pawn of Ganon or purposely working for him,note It's also stated fairly early on that his goal is to free Ganon, rather than being a plot twist 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, Ganon quite possibly hijacked ALttP from himself.
In the Oracle games, the Twinrova sisters, Kotake and Koume, are the real Big Bads. Ganon is the Final Boss, but he does not directly have a hand in the plot, making him more of a Bigger Bad.
Four Swords Adventures is a odd mixture of this and The Man Behind the Man. Vaati is a reccurring 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.
Played with in Skyward Sword, as Ganon doesn't appear in person, but the ending reveals that the spirit of Ganon that keeps pursuing Zelda and Link's descendants is the incarnation of the hatred of Demise. Thus in an ironic twist, everything Ganon has done has been essentially hijacked by Demise. Also counts as Fridge Brilliance as Demise doesn't mention Ganon by name. This not only explains how Ganondorf can be the same character in multiple games yet sport different visual designs, and have different Ganon forms, but also implies that other, unrelated Zelda villains could also be Demise, most likely Malladus from Spirit Tracks. It also adds an added layer of intrigue to possible future Zelda villains who don't lose out to Ganon that game/timeline.
In The Legend of Zelda: A Link Between Worlds, it's actually inverted. 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. Then Hilda is revealed to be the Bigger Bad all along, and you think Yuga's role as Big Bad is going to to stop there, but he actually betrays Hilda, turns her into a painting and absorbs her power, once again keeping his position. Hijacked by Yuganon, indeed.
Anime and Manga
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.
Played with in the Cell 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 never mentioned in the original arc.
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.
Naruto does this with Orochimaru during part one's interminable filler seasons - they even retcon Mizuki, from the first chapter, into having been operating under the orders of the aforesaid baddie.
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.
The US dub of Pokémon Heroes made Annie and Oakley agents of Team Rocket when in the original they had no association with them.
A key plot element in Umineko no Naku Koro ni, also inverted. Most of End of the Golden Witch involves Battler trying to keep the role as protagonist and Bernkastel doing the hijacking.
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.
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 Avengers robotic villain Ultron has this as pretty much his trademark plot. In every single issue he EVER shows up in, he never appears to be the main antagonist the Avengers will be up against, rather evidence will point it to being someone else, before Ultron dramatically reveals himself. Even in his very first appearance as a villain, he wore a disguise and diverted suspicion to Jarvis of all people (successfully at that) before it was revealed it was he.
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).
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.
The Death of Superman did this with its final storyline Reign of the Supermen, the story starts out normally with the first two issues of each title attempting to endear us to the four Supermen. Then come the halfway point of the third month when the Cyborg Superman decides to ventilate the Eradicator and allow Coast City to be destroyed by Mongul. Then, it turns out the Cyborg Superman was actually a very minor character who was an expy of Reed Richards!
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.
A flaw in the later seasons of the ElfQuest 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. In the distant future, residual taint from her evil magics at Blue Mountain is the focus of a major subplot.
In Grendel, Pope Innocent XLII, the Big Bad of the 26th century arc, turns out to be Tujiro, the vampire serial killer from the 21st century arc.
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.
Century: 1969, the penultimate volume of The League of Extraordinary Gentlemen, ends with the revelation that the Big Bad Oliver Haddo survived his confrontation with the League by escaping to the astral plane and possessing the body of a young Thomas M. Riddle, aka Voldemort (the most well-known literary villain of the 21st century). Sure enough, Century: 2009, the final installment, has the League facing off against Haddo inhabiting Voldemort's body.
During the "Dead End Kids" arc, the Runaways end up in New York City in 1907. While there, they are told that the criminal underworld is supposedly run by Maneater (a sort of predecessor to the Kingpin) and the Sinners. Chase and Xavin later discover that the Sinners are actually answering to Dale and Stacy Yorkes, the parents of Chase's dead girlfriend, and enemies to the Runaways. They are understandably displeased when they find out that Gert's dead in 2007...
In the Sin City tale Hell And Back, Wallenquist was revealed as the Colonel's boss with the Colonel's main assassin answering directly to him.
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 Ultimate Marvel, Dr. Doom has pulled this twice to date: in the Ultimate Power miniseries and in The Ultimates vol. 3 ''. 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.
Double subverted in Perfection Is Overrated. Near the end of the fic, the Usurper, in a last bid at defeating the Himes and ruling the world, possesses the Obsidian Lord, who had initially seemed to be the final antagonist the Himes would face. When the Usurper's remaining minions are defeated and the Obsidian Lord is forced out of Reito's body, the Obsidian Lord breaks free of the Usurper's control, killing him, before having one last confrontation with the Himes.
Total Drama fan season Total Drama Luxury Tour briefly sets up Alejandro, who was the Big Bad of the season immediately before it, as the main antagonist for the first few chapters. Then he's voted off pretty early thanks to Noah, and for the majority of the story following that, Duncan is geared towards being the villain. And then Alejandro simply bribes his way back on the game, takes a serious level in jerkass, and takes over as the main villain, especially after Duncan himself is eliminated near the end.
Spider-Man 3 has a form of this. Turns out the guy Spidey killed in the first movie didn't kill Uncle Ben after all, The Sandman did! We never see Uncle Ben getting shot in the original, but it still gives no indication that there was more than one robber involved.
In Captain America: The Winter Soldier, HYDRA has actually been ressurected amongst SHIELD's ranks ever since the agency's own formation, the mastermind this time being the Red Skull's right-hand man in Captain America: The First Avenger, Arnim Zola. This also puts into light certain events in the Iron Man films, such as the deaths of Tony's parents and Senator Stern wanting to get his hands on Tony's tech. The former is actually a Make It Look Like an Accident engineered by HYDRA (since Howard Stark was one of SHIELD's founders) while Stern is in fact one of many HYDRA agents.
In Artemis Fowl: The Time Paradox, the apparent villain-of-the-day (or yesterday) Damon Kronski turns out to be the pawn of Opal Koboi.
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. For example, the Foreman with the bad wig turns out to be the Bald Man With The Big Nose, the doctor with the "unusually solid hands" turns out to be the Hook-Handed Man, and Officer Lucinda with her "lipsticked smile" turns out to be Esme Squalor. 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.
In the last book, there is Ishamel, a man the siblings never heard about from anyone on the vast V.F.D. organization (where everyone seems to know everyone) and was able to seemingly defeat both the Baudelaires and Olaf - and Kit Snicket. In the end, it also looked like he is the only one of the original people on the island to make it alive to the continent.
In the first three Black Company books, Dominator is a well-known Bigger Bad to Lady's Big Bad, so when he tries to hijack the plot in every book, it's this trope in-universe. Subverted later in the series with new Big Bad well, Big Bad Wannabe 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.
Books Of Bayern: In the fourth book, Selia 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.
In The Crystal Prison, the second book in the Deptford Mice trilogy, Nicodemus, the spirit controlling Madam Akkikuyu turns out to be Jupiter, the evil god from the previous book.
Substitute Ganon with Takhisis and you have the entire War of Souls trilogy in the Dragonlance series.
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.
Kitty Takes a Holiday is an interesting example in that "Ganon" is a non-personified antagonist. The opening chapters are about Kitty trying to keep Ben's new lycanthropy infection from driving him to suicide. After the initial crisis is resolved, the resultant Rescue Romance is a B-plot through the remainder of the book. Meanwhile, the A-plot eventually leads Kitty and Ben to The Man Behind the Man. It turns out that neither party can beat the other, so the good guys have to Know When to Fold 'Em. The stress of failure causes Ben to wolf out, and the climax of the novel is Kitty chasing Werewolf-Ben through the woods, trying to find him and calm him down.
At least from the perspective of the majority of the world, this is what Satan does to the Antichrist in the Left Behind series.
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 by the Forkrul Assail, a Knight Templar race of Abusive Precursors, who intend to use it to scour the world of humanity, which they see as unsalvageably corrupt. While the Forkrul Assail 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.
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.
In the Vorkosigan Saga, The Vor Game is a good example. The entire plot is Hijacked by Cetaganda.
Warrior Cats: Sol is probably the only villain in the entire series that isn't somehow connected to Tigerstar.
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!
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.
In the Season Eight comics, it turns out Twilight is actually Angel.
Dark Willow reappears in the Time of Your Life arc of Season 8.
Happens in the fifth season of Chuck. Clyde Decker is set up at the beginning of the season to be operating a conspiracy by a faction of the CIA intent on destroying Chuck Bartowski, his friends, and his family. Midway through the season it's revealed that Daniel Shaw, who underwent a Face-Heel Turn halfway through the third season and tried to take over the CIA before the team stopped him, has been pulling Decker's strings (via blackmail over Decker's corrupt past) all along. And then that gets hijacked by Quinn, who it's revealed was behind everyone Chuck had been dealing with out of spite because Chuck "stole" the Intersect from him (Quinn was selected to be the Intersect agent, but after Bryce stole it and sent it to Chuck, Quinn was sent into the field without it, captured, and tortured. Yes, there was a bit of Sanity Slippage involved).
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.
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.
Done twice in "Frontier in Space", in which the Ogrons are quickly revealed to be working for the Master (in Roger Delgado's last story before his death), who turns out in the final episode to have been working for the Daleks.
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 Season 7, the Great Intelligence being behind everything would count as this. Turns out the villains in the Christmas special and the Bells of Saint John were just The Dragon to him.
The second, third, and fourth volumes of Heroes were 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, Adam Monroe, Arthur Petrelli, and Emile Danko, 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.
Ultimately subverted in the final volume, where Samuel Sullivan is established as the Big Bad fairly early on and keeps that title right up until the finale. Not only does he easily defeat Sylar the one time they fight, but Sylar has Heel-Face Turn that actually seems to stick this time.
And in the old days, Shocker's Great Leader turned out to be behind any number of evil organizations. At least now it takes an actual revival of Shocker for this kind of thing to happen; in the old days, it'd be Goro Naya popping up to say "Undead? Makamou? Greeed? All my plan even if there's no freakin' way." at the end of a series that never seemed to have anything to do with him or those others.
In LOST, the first antagonist encountered in the series is the Smoke Monster, which had been terrorizing the survivors since they first crashed on the Island, long before we even know about the Others. Early on, it was assumed that it was a raging beast, but later, we learned it was much more than that when it was discovered that it could assume the form of deceased characters. However, it only appeared in a few episodes and seemed to take a backseat to other antagonists such as Ben, the Others, Widmore, etc. After seasons of debating who the Big Bad would be, the season five finale introduced an unnamed man, The Man in Black, who is Jacob's enemy, vowing to kill him, and at the end of the episode, we learn he was manipulating everyone, especially Ben and Locke, the whole time in order to accomplish this. It is revealed in the season six premiere that this man was none other than the Smoke Monster, making him the Big Bad since the very first episode.
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.
In season 8 of Stargate SG-1, Ba'al takes control of Anubis's remaining forces after the destruction of Anubis's fleet during the invasion of Earth, and uses his superior Kull Warriors to succesfully wage war on all the other Goa'uld combined. Anubis reappears on Earth, but gets stuck on a frozen planet in a dying host body. At the end of the first part of "Reckoning", Ba'al reveals to O'Neill that Anubis is back in command of the largest Goa'uld faction, and that he was serving him for a while now.
In Star Trek: Deep Space Nine, the revelation that the Breen were working for the Dominion was done in a similar fashion. And that the Orion Syndicate had been working with the Dominion too, in an earlier episode.
The conclusion of Tin Man reveals that the Big BadPrincess Azkadellia is actually a descendent of Dorothy Gale who was possessed by the spirit of the original Wicked Witch as a child. D.G. (who's actually Azkadellia's sister) frees her from the Witch's influence in the last episode's final act, and she reverts to her original personality.
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 Adolf Hitler. When Hitler reveals his identity to the neo-Nazi leader, he stops giving advice and starts giving orders.
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. Once the final monster is destroyed, the unknown hand reveals himself to be an entire evil Ultra known as "Dark Zagi".
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 the final season of 24, the Russians, who were behind the deaths of Omar Hassan and Renee Walker, were hijacked by Season 5's Big Bad, CharlesLogan. Season 7 had teased Logan pulling this by constantly referencing him and having Tony go on a Roaring Rampage of Revenge, but unfortunately, it turns out that some random guy named Alan Wilson was Tony's target and the one behind multiple conspiracies.
Also, in The Game, Max, the man behind Season 2's events, is the Big Bad.
Subverted in season six; it seems like the Chinese are pulling this, but Phillip Bauer turns out to be the actual antagonist.
Throughout The Bible, everyone who commits an act of sin can be said to be tempted by Satan, directly or otherwise. However, the Book of James doesn't buy blaming Satan (or God, for that matter) as a Freudian Excuse, though:
When tempted, no one should say, “God is tempting me.” For God cannot be tempted by evil, nor does he tempt anyone; but each person is tempted when they are dragged away by their own evil desire and enticed.
In Norse Mythology, everything in creation (even the flora) have to shed tears to bring the God Baldr back to life but there is one Frost Giantess who refuses and as a result, he can't. The Frost Giantess turns out to be Loki, who killed Baldr in the first place, in disguise.
Christian did this to WWECW upon his 2009 return. In fact, one could argue that he and Shelton Benjamin were the only reason anyone would watch the show by that point.
In early 1993 WWE, manager Harvey Wippleman was not happy about how The Undertaker had defeated Wippleman's man Kamala in the Casket Match at Survivor Series 92, leading to Kamala's face turn and siding with Reverend Slick. On the January 16, 1993 (taped December 14, 1992) episode of WWF Superstars, Wippleman announced that the WWF would never be the same after he dropped "the big bomb." At the Royal Rumble, January 24, 1993, Wippleman revealed what "the big bomb" was: the 7'7" (billed as 8'0"), 400 lbs.+ the Giant Gonzales (real name Jorge Gonzales, formerly WCWbabyface El Gigante), who interfered in the match and eliminated the Undertaker! May he rest in peace.
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.
In 2003 WWE, Sean O'Haire was starting a Corrupter/Devil's Advocate gimmick, where he would tell people to do unusual or outrageous things, topping it off with his Catch Phrase, "I'm not telling you anything that you don't already know." On the February 6th SmackDown! he convinced Brian Kendrick to streak after A-TrainSquashed Shannon Moore. On the March 13th show, he convinced Dawn Marie, a Heel herself, to "flash" the crowdnote This was the same night that Torrie Wilson, Stacy Keibler and Nidia all appeared on the Girls Gone Wild PPV, though none of them actually got naked. Dawn had tape over her breasts and the rope was in the way. Then "Rowdy" Roddy Piper returned to WWE during the Hulk Hogan vs. Vince McMahon match at WrestleMania XIX on March 30th as a heel, attacking both guys. O'Haire got turned into Piper's lackey as part of the whole ridiculous feud with Hogan/Stephanie McMahon/Zach Gowen vs. Vince/Piper/Sable/O'Haire/A-Train/The Big Show and maybe some other people. Even after Piper was fired in June, O'Haire never really got any kind of chance to revisit the gimmick and left in 2004.
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 WWFnote Sting and UW started their careers together in California before going to Memphis as the Freedom Fighters and then to "Cowboy" Bill Watts' Mid-South/UWF as the Blade Runners, Flash and Rock, before going their separate ways. When it didn't work, they shoehorned Flair in instead.
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.
In 1999, WWE featured a long and convoluted storyline about The Undertaker and his Ministry Of Darkness attempting to seize control of WWE from former bad guyVince 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.
After the release of Infernals in the second edition of Exalted, the Ebon Dragon seemed to have his hand in everything. He created the Unconquered Sun (Okay, that had been there since early first edition). He made contact with the Neverborn for the purposes of creating the Infernal AND Abyssal Exalted. He abducted the Scarlet Empress. He contacted the Viator of Nullspace and set him on his current quest to remake the Great Maker. Certain lines in Return of the Scarlet Empress—the storyline in which one has at least four other Yozis to worry about, along with their own forces and those with the Realm, and he still manages to arise as the clear dominant villain of the entire game—even strongly suggest he was behind the Great Curse.
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.
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. It worked.
Video Games (Excluding Ganon)
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.
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, Strange ended up being a pawn of Ra's, who you already beat earlier ingame, and both of them died in the same cutscene, before the final confrontation with Joker.
In Origins, trailers hyped up a relatively unknown to non-comic fans villain, Black Mask, as the Big Bad who hired eight assassins to kill Batman. It was really Joker pretending to be Black Mask the whole time.
In BioShock the first part of the game focuses on you hunting down and killing Andrew Ryan, only to learn that all the events guiding you to kill Ryan were crafted by Mission Control, who is the supposedly-dead Frank Fontaine.
The Bubble BobblespinoffBust-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.
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.
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? That's Dracula. That vampire you fought earlier in the game was a faker.
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 evencanonically became Dracula.
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.
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 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 the daemon, inadvertently released by Gabriel back in the end of the first game.
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.
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.
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.
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.
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 the PS2 video game Fullmetal Alchemist: 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 Bigger Bad and the true instigator of the events.
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 story 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.
Kingdom Hearts, thanks to its confusingcosmology, has a rather weird example: the Big Bad of the entire series is Xehanort, but he appears in many different incarnations over the series. Maleficent was presumed to be the Big Bad of the first game, until the original villain Ansem was revealed to be the true mastermind manipulating her. The next two games revealed "Ansem" was actually Xehanort's Heartless, and his Nobody, Xemnas, was the leader of Organization XIII and thus the villain of II. 358/2 Days technically had no clear villain, but it did have Xemnas and Saix as antagonistic forces, and Birth By Sleep revealed the original Xehanort was Master Xehanort, who became the Xehanort that was split into Ansem and Xemnas when he committed Grand Theft Me on Terra's body. Dream Drop Distance then had a new Xehanort as the villain, who turned out to be a younger Master Xehanort travelled forward in time from the past. The bottom line of all this, every main villain has either been a Xehanort or his accomplice or Unwitting Pawn, and his connection the villain of the latest game is always played as a plot twist. Dream Drop Distance and promotional materials for the next game Kingdom Hearts III say that the revived Master Xehanort is the main villain for the game, making it the first time Word of God doesn't try to hide his involvement. There are two semi-exceptions: The villains of Chain of Memories are rebelling against Xemnas, and the closest Kingdom Hearts Coded gets to a true villain is connected to Sora, not Xehanort.
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. He then partially hijacks that game 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.
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 minigames work is the final boss and has no clue who Jack is. Oh, and he's 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 pretty much shrugged and said "It's probably Reapers" in the first conversation about the Collectors.
This is Dr. Wily's trademark tactic in the Mega Man (Classic) 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 7 is that the game begins with Wily being arrested, but his robots activate themselves and free him. Also does it in Mega Man V for the Game Boy with the Star Droids though in a bit of a twist, he is not the final boss of this game. 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 Mega Man X2 onwards, to the point it's a twist that he isn't the Big Bad of Mega Man X8. It gets lampshaded in Mega Man X4 when Split Mushroom responds to a demand to reveal the mastermind behind the game's plot with his meme-tasticCatch Phrase "Take a wild guess", after which his lifebar appears, blatantly carrying Sigma'slogo, unlike previous bosses. It's also subverted in Mega Man X6, when the Big Bad was not Sigma, it was Gate, and Gate resurrected Sigma to use him to destroy X, but Sigma Came Back Wrong and was obviously not the controlling force behind the plot.
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 entireX 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. There's also fan theories that Serges and Isoc, each originating from different games in the X series, are either Dr. Wily somehow, or that like Sigma, Wily's consciousness endures and finds host bodies to act through.
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 third and fourth games, uses a robot (Zero's original body, specifically) that Wily likely designed or built. And of course, there's another theory that Dr. Weil is Wily.
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 somehow 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.
In the Mega Man Battle Network games (which are an Alternate Universe 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, lead by Wily's son.
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.
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 Bigger Bad.
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 villian.
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.
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 subverts this they have nothing to do with the plot, simply serving as Easter Eggs to observant players.
A notable inversion, in that once the Sonic Adventure-era titles started rolling out, Eggman had a bad habit of getting upstaged when it came time for the Final Boss fight, something that's only being rectified with more recent games.
Sonic Lost World has Sonic and Eggman team up for an Enemy Mine early in the game, Eggman looking upstaged by the game's villains for the bulk of the game, but at the start of the last area, Eggman fakes his death and sneaks off to complete his final mech in time to be the game's 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...
Andross also pulled this one in Star Fox Adventures. You even have to beat him the same way as in 64.
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.
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 super hero. Ratchet ends up having to save the galaxy instead after he screws it up.
With no real buildupnote he appears on the box art, and that's it, Carnage randomly appears as the final boss of Venom/Spider-Man: Separation Anxiety.
Super Robot Wars has an equivalent to Ganon in its midst known as Euzeth Gozzo. In the Alpha series, it seems he recalls his time from Sasuken (a side game in which he was the final boss), but only on his death do you find that he brainwashed Ingram, Viletta, and Levi into serving him, and that even if he dies the main Balmar force would take over eventually (cue Alpha 3 where they try to do just that). Then, ten years later, in Super Robot Wars Original Generation the 2nd, he pulls a MASSIVE gambit to usurp Irui Gan Edan and become the True Final Boss.
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.
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.
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 Sycophantic Servant for Kil'jaeden.
Kil'jaeden and Archimonde were also behind most of the events of the RTSWarcraft 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'sBig Bad Deathwing and yet-to-be-seen Queen Azshara.
On Zero the Kamikaze Squirrel, the mastermind behind Jaques Le Sheets' scheme is Edgar Ektor.
A complicated quadruple example in the Metal Gear series. In Metal Gear Solid 2, Revolver Ocelot (already a villian from Metal Gear Solid) reveals himself to be a spy for The Patriots, but then get's possessed by the hand of Liquid Snake, the Big Bad of Metal Gear Solid and goes rogue. Then in Metal Gear Solid 4, 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.
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 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 Frans "I was pretty sure you were dead" Rayner, the main villain of the D.A.R.E plotline from years ago.
In Sluggy Freelance, the "wraiths" attacking the other dimension in the "Aylee" arc are actually members of Aylee's species, who, not counting Aylee's evil clone, hadn't appeared since Aylee was introduced 10 years previously.
Not to mention several dangerous situations set up by demons who appear to be fragments of K'Z'K', the demonic Big Bad from several early arcs.
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 Arby 'n' the Chief, Chaos Theosis, the main antagonists of Season 6, were actually working for Trent Donnovich, who was the main antagonist of Season 5.
In Chaos Fighters II-Chemical Siege, after the true villain is revealed as Etphan Signis, when Enrei and Gareia finished him, it was revealed that Thanic Snader, the Big Bad of Cyberion Strike, did everything, including mind controlling Etphan so that he can leave Etphan doing the dirty work.
In Ducktalez 7, The Beagle Boys were run by Julia Roberts, who was reconstructed by Eric Roberts after the sun nearly killed Julia in 3.
At the conclusion of Moonstuck, the "Nightmare Woona" who has caused most of the trouble is revealed to actually be Discord.
In There Will Be Brawl, we do end up getting a non-Zelda example for the Trope Namer, Ganondorf. Then given another example in-universe when he is hijacked by Kirby, who had been a problem to the kingdoms in the past.
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.
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 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.
Season 2 is even more complex; starts 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 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.
In Gargoyles, for a large chunk midway through the series a group of three god-like beingscalled 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.
In Justice League Unlimited, 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.
However, the trope is then subverted when said Hijacker fuses with the Hijackee, except the Hijackee seems to be the dominant personality as seen in the ending of the Arc, thus creating a Big Bad Duumvirate. In many ways, it just gave a shocking way for Luthor to fight on even footing with the Justice League.
And 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 Darksied instead.
Double Subverted. When vines from the Everfree Forest started invading Ponyville and the princesses went missing in the My Little Pony: Friendship Is Magic epsisode "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.
Rocky and Bullwinkle: It doesn't matter who or what's causing trouble in Frostbite Falls or anywhere else in the world. In the end, either Boris is always going to be the one causing all the mayhem, or if he isn't the antagonist of the episode, they're going to bring him in to help them out. The exception is "The Ruby Yacht", where he does not get involved at all.
In Tintin and the Lake of Sharks (1972) based on an original story, Tintin and friends faces a criminal organization specializing in making art forgeries lead by the mysterious "Shark King". It turns out "Shark King" is Roberto Rastapopoulos, Tintin's most recurring villain.
In second season of W.I.T.C.H. 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. At least until Cedric tricked him into giving him all his powers.