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- In the Cowboy Bebop episode "Sympathy for the Devil", the Bebop crew tries to track down an old bounty head called Zebra, who seems to be masquerading as a paralyzed man living with a young boy. Only after searching the memories of one of Zebra's dying friends do the crew find that Zebra is really disabled and is in the clutches of the boy, who, due to a freak hyperspace gateway incident, doesn't age and is much older than he looks.
- InuYasha is a pretty unusual case. Early on, Naraku emerges as the main villain and orchestrates most of the plot, with various minor villains serving his ends and any setbacks are All According to Plan. His goal is to attain the Jewel of Four Souls, which will grant him a single wish, that would presumably make him invincible. Only in the final act, when he finally gets his hands on the complete Jewel, is it revealed that the MacGuffin itself was manipulating him and all others who used it towards its own ends. Even after Naraku is finally finished, the Jewel continues to be a threat until it can be destroyed.
- Tobi is introduced as not even being a member of the Akatsuki, just a particularly goofy minion of theirs. The real leader appears to be Pain. Then it's revealed Pain was only the front man of the organization and Tobi was his boss all along.
- Most of the time Black Zetsu seemed only The Dragon for Madara, imagine how Madara and all the spectators were surprised when he showed that he manipulated Madara all this time for the revival its creator Kaguya.
- In Dragon Ball GT, the villain named Baby was first introduced as the treasured creation of the evil scientist Dr. Myuu. Then it turns out that it's the other way around; Myuu and his creations were just a front to gather the newly-scattered black star dragon balls and revive the destroyed Planet Vegeta for Baby, revealed to be the king of the Tuffles — the extinct rival race of the Saiyan main characters — to reign supreme.
- Prince Demande appears to be the main villain of the second Sailor Moon arc, but over time it becomes apparent that his "advisor" Wiseman has been using him as a pawn the entire time.
- In The Avengers Issue 54, the Villain of the Week is the Crimson Cowl, leader of the reformed Masters of Evil, who kidnap Edwin Jarvis (who hasn't undergone any Character Development at the time). At the climax of the issue, it was revealed that the Crimson Cowl issuing orders from his throne was apparently a decoy robot, and the real Crimson Cowl was Jarvis himself. The events of the next issue reveal, however, that Jarvis was actually Brainwashed and Crazy, and the real mastermind was the robot, none other than Ultron, the Living Automation, in his Ultron-5 incarnation.
- Dragonheart has one that overlaps with mistaken blame: the prince Einon is given a heart transplant from a dragon to save his life. He then ascends the throne and becomes a tyrant. The protagonist believes that the dragon corrupted him and goes seeking for revenge, but the dragon claims, and Einon eventually confirms, that he was Evil All Along and used the dragon's gift for his own plans.
- In Batman Begins, a man is introduced as Ra's Al Ghul, looking every bit the namesake, with his adjutant, Henri Ducard. But before long, it becomes clear the big man is a Decoy Leader and "Ducard" is the true Ra's Al Ghul. Misdirection is, after all, one of the League of Shadows' prime tricks.
- In Fast & Furious, the front man for the drug running ring appears to be working for an unseen boss. The boss turns out to be a decoy and the front man is the actual boss and Big Bad.
- Iron Man 3 is similar to Batman Begins, in which the Mandarin is just a decoy (or to be really specific, an actor), and the apparent Dragon Aldrich Killian is revealed as the true mastermind.
- In Kamen Rider × Super Sentai: Super Hero Taisen, Emperor Marvelous and Tsukasa Kadoya, the leaders of Dai-Zangyack and Dai-Shocker respectively, turn out to have both been manipulated into killing off the Kamen Riders and Super Sentai by their supposed underlings so they could take over the world unopposed. Right after they reveal this, however, Marvelous and Tsukasa reveal that they were both well aware of what they were doing, and had only been playing along to find out what their true plans were.
- In Spy Kids, it turns out that all Floop wanted to do was make his kids' show. Mr. Minion was the mastermind.
- The Elenium:
- At first it seems that Annias is the main foe with his bid to become leader of the corrupt church, making deals with the dark god Azash and hiring the mercenary Martel to start fires throughout the continent for the Church Knights, who want to purify the corruption, to be kept busy with. But after his main gambit fails, it comes out that Martel has been pulling Annias' strings.
- Later it becomes apparent that Martel is taking orders from Azash, who is manipulating events to bring the Bhelliom out into the open for the taking.
- Continued in the sequel series The Tamuli, when Martel's lowly lackey Krager claims he was the brains of their operation all along; then, he and various other rabble-rousers are in the employ of a new villain, a god called Cyrgon who had been thought extinct (while the last part is true Krager is later confirmed to have been exaggerating more than a few things in his speech, throwing doubt on his claims to have mentored Martel).
- Later, Cyrgon is actually working for the true Big Bad, Zalasta, who has been manipulating the events of both series in his bid to get the Bhelliom for himself.
- In Book of the New Sun, two of the characters are Those Two Bad Guys, Dr. Talos and Bandanders (both cases of Meaningful Name combined with Genius Bonus). Talos, who clearly seems to be the leader, is a clever, glib Con Man with fox-like features. Baldanders clearly comes off as the subordinate and appears to be a Gentle Giant and rarely speaks. In actuality, Baldanders is some sort of Humanoid Abomination Mad Scientist who turns out to be a threatening villain, and Talos is an Artificial Human, who is his creation- the parallels to/subversion of Frankenstein's Monster are deliberate..
- In Foundation and Empire the Mule, the psychic leader of a powerful army which is derailing the Foundation's plans, is in disguise as a Court Jester for one of his underlings. He gets "rescued" by Foundationers and taken to their home planet.
- In The Sirens of Titan, the entire Army of Mars is run by underlings who command their superiors via remote control.
- The Stainless Steel Rat makes this almost fatal mistake when he first confronts criminal psychotic Angelina. Bringing down an arrest, he refuses to believe the ditzy, hysterical, beautiful airhead he sees is anything more than a low-level Mook and gangster's moll. He therefore ignores her and focuses on arresting her accomplice - who is brooding, intense-eyed and unshaven and looks like an Evil Genius. In the confusion, she escapes, having conned diGriz into thinking she's insignificant. While he is arresting the hired help, she slays two policemen and steals an escape pod, evading laser fire and tractor beams with some skilled stunt-flying.
- In Worm, Doctor Mother appears to be in control of Cauldron and does all of the talking, with Contessa being her bodyguard. It is later revealed that Doctor Mother is nothing more than a manager and of rather little importance, while Contessa is the one who makes decisions based on her power to know the way to victory.
- In the New Jedi Order, Supreme Overlord Shimrra is always accompanied by his personal slave and jester Onimi; though Shimrra will sometimes send Onimi to act as his proxy outside his court, everyone agrees that when not acting on the Supreme Overlord's direct orders, Onimi is obnoxious and rather perverted, but essentially harmless. Then the ending of the novel Destiny's Way makes it clear Onimi is smarter than he looks and has some sort of link with Shimrra. Then the climax of the final volume, The Unifying Force, reveals that Onimi was telepathically controlling Shimrra the whole time, and is the true Big Bad of the entire series.
- Being Human (UK): In series two, Professor Jaggat is introduced secretly as the scientific mastermind behind the purging of the werewolves, with Kemp as her public face - her dragon. However, towards the end, we find out Jaggat is just the one Kemp goes to when he needs to find a method of killing a werewolf or vampire; Jaggat is in fact the dragon to him, and is dragging her feet on the verge of a Heel–Face Turn. Occasionally, she tries to take over, too.
- Star Trek: The Original Series: In "Patterns of Force", a society of Human Aliens has emulated the regime of Nazi Germany, complete with atrocities committed for racial and cultural motives. The officers of the regime carry out the orders of their Fuhrer, who they only see via television broadcast. It turns out later that the Fuhrer was drugged and under the control of his Deputy. It was the Deputy Fuhrer who was really responsible for giving orders to the Nazi forces, while the true Fuhrer had good intentions all along.
- The Wire: The crime lord known only as "The Greek" sits in on conversations with other gangsters by having his actual second-in-command Spiros do the talking and disguising himself as one of his lackeys.
- In the Doctor Who serial "The Pirate Planet", the stereotypically hammy Big Bad is eventually revealed to be a patsy of his nurse, who is in fact a holographic projection of the moribund Queen Xanxia—the "stealing planets" aspect is a way to keep her time dams from failing.
- In "Day of the Daleks," the Controller of the Britain region serves as this to the Daleks—in fact, his whole family had served as this for generations. Interestingly, the Controller states that he doesn't necessarily like his masters, but feels that he doesn't see much choice in the matter. Also, as the Doctor later points out, "They would always have found someone."
- In the original Baldur's Gate, you are led to believe that Sarevok is The Dragon to the leaders of the Iron Throne company (specifically, to his father—the "CEO" of Iron Throne), but in reality, he has been the real mastermind all along and they are actually his pawns.
- Escape from Monkey Island features the return of regular villain LeChuck in a bid to con the feckless inhabitants of Mêlée Island into voting him the new governor, plus the introduction of amoral land-grabbing entrepreneur Ozzy Mandrill. It's obvious they're working together, but only in act 3 when they have a confrontation with the Guybrushes does it come out that LeChuck is working for Ozzy and not the other way around.
- The Legend of Zelda: Majora's Mask: The Skull Kid, lonely and frustrated, found an ancient and powerful mask, using it to play cruel tricks, culminating with summoning the moon to fall toward the earth. So it seems. But somewhere along the way, the evil mask started calling the shots; in the final confrontation, Majora's Mask throws the Skull Kid away like an useless puppet, and carries on with its plan as if nothing had happened.
- Fire Emblem Elibe While the player has already been informed while the lords have not, Marquess Laus seems to be the enemy in charge of it all. Once the party learns of Nergal and Ephidel, however, the surprise quickly turns on Marquess Laus himself, the only person who didn't know he was the victim of the trope.
- In Jade Empire, it is widely believed that Deaths Hand is corrupting The Emperor. Eventually it is revealed that the latter has bound the former's soul and was controlling him all along.
- Halfway through Pokémon Black and White, N tells the player that he is the king of Team Plasma, meaning that the Seven Sages all defer to him. However, at the end of the game it's revealed that one of the sages, Ghetsis, has been orchestrating everything and had been manipulating N all along and only let him believe he was in charge.
- Paper Mario:
- Dimentio from Super Paper Mario poses himself as a minion of Count Bleck, but he turns out to be the main villain of the game. What makes this different from Dimentio being The Starscream is his supposed involvement with the creation of the Dark Prognosticus, which states that a man similar to Dimentio was part of the prophecy Bleck followed. This ended up convincing Bleck to add Dimentio to his organization (which would mean that Bleck was being manipulated from the start).
- Zig zagged with Beldam from Paper Mario: The Thousand-Year Door, who appears to be just a minion of Grodus, the supposed Big Bad of the game, but it's then revealed that she was only working with him in order to further her plans of reviving the Shadow Queen - whom she is actually a loyal underling of.
- Earthbound: Porky/Pokey has shades of this as it is implied that he's the one using Giygas instead of the other way around, if only because by the time you face him Giygas is completely and irrevocably insane.
- Final Fantasy XIV: The Shadows of Mhach storyline revolves around various demonic entities trying to resurrect the Void Queen. However, after she is slain by the heroes Diabolos, who was orchestrating the entire event, revealed that the only reason he orchestrated the events which spanned several thousand years was so that he could eventually kill the Void Queen himself and claim her power as his own.
- Final Fantasy XV: Ardyn, as in the guy who constantly bugged you through the first five hours of the game and even took a selfie with you, is the Big Bad. Not the Emperor, just this flamboyant messenger guy.
- Mass Effect: Saren, a rogue SPECTRE agent, appears to be the main villain of the game who's working to summon the Reapers from dark space for vague reasons that may have something to do with his racism against humans. Throughout the game he rides around in Sovereign, a spaceship so advanced that it's assumed to be a Reaper invention. Then comes the big reveal that Sovereign is not a mindless Reaper spaceship, he's an actual Reaper, and the true mastermind of Saren's plot.
- The Order of the Stick:
- Tarquin has set himself up as The Dragon to the Empress of Blood, who is literally a large red dragon. It soon becomes clear, however, that the Empress of Blood is not only a figurehead but also a pawn in Tarquin's plot to rule the entire continent from the shadows.
- Redcloak was Demoted to Dragon after Xykon became a lich, complete with a rather nasty "The Reason You Suck" Speech. To Redcloak, though, Xykon is just a powerful and very dangerous tool for accomplishing his goals. Xykon is a lazy goofball of a villain, and Redcloak has been controlling him through several strings to keep him moving in the direction that Redcloak wants him moving in, as he explains to Tsukiko at one point. Sometimes Redcloak's control slips a bit, as emphasized by Xykon banning him from regenerating his eye.
- In Spacetrawler, Kuu-Drahc is initially presented as the big bad, as he's the highest official authority in the known galaxy. In the senate scenes, an unnamed character stands just behind Kuu-Drahc, looking for all the world like a secretary or advisor. Turns out he's actually Qwahntoo, the real power behind the galactic government and the true big bad of the comic.
- In Seasons 11-13 of Red vs. Blue, both the New Republic of Chorus and the Federal Army of Chorus are being manipulated into waging war with each other by the bounty hunters they hired, Locus and Felix, who are, in turn, revealed to be working for someone else looking to claim the planet for his liking.
- The first episode gives the impression that Roman Torchwick is the main villain and that the mysterious woman who flew his airship and fought off an enemy huntress on his behalf is another one of his minions. Later on the woman is revealed to be Torchwick's boss, Cinder Fall.
- Later on, Corsac & Fennec, two twins who work for the White Fang and have been allied with Adam for a while appear to be only the spokesperson for the Menagerie faction of the White Fang and silent supporters of Adam. When alone, they speak of replacing Adam if he becomes to unhinged and hard to control, with implications they were the ones to have given him as much powers as he has now..