The Man Behind the Man aka: The Man Behind The Woman
Being a Chessmaster doesn't always mean you're in charge.
Solidus: I'll leave you alive, Jack, because you're still manipulable! Fortune: Speaking of manipulation, it's time for me to steal Arsenal since I've been manipulating you from the start! Solidus: Actually, I tricked Ocelot into manipulating you into manipulating me! Ocelot: Fools! I've been manipulating everything from behind the scenes! Magic Hand: But actually, I've been manipulating you! Raiden: Alright, this has officially become a load of crap.
When a character previously positioned as a Big Bad is revealed in fact to be either a Disc One Final Boss or The Dragon, The Man Behind the Man shows his (or her, or its) face.
The Man has deeper problems, deeper motives, and so much power that the heroes will have to go through another round of dungeon diving just to stand a chance. When he reveals his reasons for being evil, expect the theme of the plot to unfold quickly and dramatically.
In many genres, the Man Behind the Man often has more sinister and apocalyptic goals than his predecessor. For example, while a puppet king or greedy corporation may want to take over the world, the real Big Bad may want to destroy the world, or even erase all of existence.
Sufficiently complex plots may involve The ManBehind The Man Behind The Man and so forth; the Sorting Algorithm of Evil usually, but not always, applies in these cases.
Can be reversed as "The Man In Front Of The Man", in which case a person you thought was the Big Bad's crony turns out to be the real Big Bad. See also Bastard Understudy and Dragon Ascendant. May be the one pulling the strings of the Puppet King.
Contrast Chessmaster Sidekick and Decoy Leader. In some (unsatisfying) occasions, The Man Behind The Man may be The Man Behind the Curtain. If there is no first man to begin with, or the first man is very obviously not the Big Bad, it's a Hidden Villain. If the mastermind turns out to be an innocuous character who was quickly overlooked, then it's a case of The Dog Was the Mastermind. If the new Big Bad is revealed to be subordinate to an old one, then the plot has been Hijacked by Ganon.
Compare and contrast Bigger Bad, where a villain more powerful than the Big Bad exists, but is either not personally involved in the plot or is not a "person" to begin with. Not to do with a Gambit Pileup though you might get one if everyone is trying to manipulate each other.
Rarely involves The Man. This trope tends to come into play with terrorist (Western or otherwise) and/or African villains being implied to be supported by Red China or white characters (normally a Corrupt Corporate Executive).
Because this trope is often used as The Reveal whenever it appears, beware of spoilers.
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Bleach: All hints pointed to Gin being the Big Bad, but after Aizen is revealed to be alive, he impales his loving vice captain and walks away with Gin following him obediently. It's made even more shocking by the prior implication that they were enemies, and that the former had killed the latter. It gets even deeper than that. Aizen claims he's basically the man behind the entire series. Ichigo (and Uryu, for that matter), wouldn't have been conceived if not for Aizen, because he's the reason why Isshin and Masaki even met in the first place.
In the Shusuke Amagai arc, it's pressumed that Kumoi wants to kill Lurichiyo and control the Kasumioji clan, but then when the confrontation comes, Komoi, Amagai appears out of nowhere, kills him, kidnaps Lurichiyo, and then proceeds to let everyone know his plans to kill Yamamoto, and he used Kumoi and the entire Kasumioji clan to get his hands on a weapon that somehow disables all but his zanpaktou so he could kill Yamamoto with it. Of course, Ichigo proceeds to save the day.
Combattler V: Halfway through the series it was revealed that Big Bad Oreana was working for Empress Janera.
In Fullmetal Alchemist, at first it seems like the homunculi are simply manipulating the country of Amestris because the Fuhrer, King Bradley, is the homunculus Wrath. Then we find out that Bradley himself is simply the result of an experiment by Father, and that Father has been controlling the entire country behind the scenes since the very day it was established 400 years prior. Most of the military's upper command is fully aware of this fact.
The first anime has a similar scenario, although it differs in key areas. Dante is the mastermind of this conspiracy and controls the government through Bradley, her ultimate creation. Once the Philosopher Stone that Hohenheim left her began to diminish, she infiltrated the government in order to facilitate the creation of a new one. Unlike in the manga, only Bradley and Tucker seem to be aware of her existence.
Near the end of Excel♥Saga, the head of ACROSS — the organization Il Palazzo serves — is revealed to be a previously-established character known only as "That Man". He makes reference to being one of the "ACROSS Six," the other five of whom are revealed in the unaired final episode to be "This Man, That Man There, That Man Over Here, This Man Over There, and This Man Over Here."
The Mazinger trilogy played much with this trope:
Mazinger Z: In the original manga, Baron Ashura shows up before Dr. Hell, leading several Mechanical Beasts and the Iron Masks troops and calling it "Ashura's army". In that chapter he seemed like the Big Bad, but one chapter after Dr. Hell is introduced and we learnt Hell was behind the whole operation and he is the real Big Bad.
In the anime, Archduke Gorgon was apparently a Dr. Hell's ally. In the last chapters we learnt he was a Dragon with an Agenda was working for a Bigger Bad, Great General of Darkness/Ankoku Daishogun. Likewise...
Great Mazinger: In the Mazinger-Z versus Great General of Darkness movie it is said the legions of Mykene Warrior Monsters are commanded by Great General of Darkness. He seems to be the supreme leader of the Mykene Empire. In first episode of Great Mazinger we learnt he is the supreme commander of the Mykene army, and he is under the orders of the Emperor of Darkness (also known like Hades).
UFO Robo Grendizer: In the original manga, Blackie is the first Vegan commander in showing up, and he seems being behind the invasion. However, in the next chapter Big Bad King Vega and Dragon-in-Chief Gandal (commander of the armies tasked with the invasion) are introduced.
In Sailor Moon, every story arc has this type of villain behind that storyline's recurring villains. The Dark Kingdom has Queen Metallia, the Black Moon has Wise Man (and even earlier, Prince Demand is behind Rubeus and the Ayakashi Sisters), the Death Busters have Master Pharaoh 90, the Dead Moon Circus has Queen Nehellenia, and Shadow Galactica has Chaos. The only time this doesn't happen is during the Makaiju filler arc in the anime, where the aliens and the Makaiju are working entirely alone.
The manga practically makes a matroshka doll of villainy as not only does each story arc feature the same series of villains behind villains as the anime does, but the final story arc one-ups them all as in the manga, the final villain is still Chaos, but in this storyline, Chaos itself has been repeatedly incarnated into all the previous Big Bad villains as well and Sailor Moon was merely fighting the same villain for a fifth time in a new form.
In the musical adaptations of the series, Chaos is downgraded to Galaxia's subordinate/jester, and not even a true dragon. But he still turns out to be The Man in Front of the Woman.
Mermaid Melody Pichi Pichi Pitch did this every season. In fact, in both seasons, we had a Double Subversion of this trope. Season one had Gaito (Gakuto and Gackto in the manga), who was working for Sara, who did a Heel-Face Turn, leaving Gaito as a worse Big Bad than Sara was. Season two had Michel's sidekick Fuku appear to be above him but below "That Man", but in the end, That Man was also manipulated by Fuku.
Digimon: In the second season, we started off with the Digimon Emperor, who later did a Heel-Face Turn and who it was revealed was the pawn of two other villains. They in turn were working for another, who was actually possessed by still another. It gets even weirder when you realize that some of the Fake Bosses' plans didn't jive well with those of the big man (Malo Myotismon). So, either Malo had one extremely bizarre Gambit Roulette going that he never bothered to explain, or the writers simply decided to fall back on Hijacked by Ganon.
The fourth season had Cherubimon who went corrupt,but it turned out that Lucemon corrupted him and two other Digimon called the Royal Knights into collecting data so he could return
Uchiha Obito in Naruto, known by the alias Tobi, pulled this off in three separate instances. He used Akatsuki to further his own plans, with Pain as a willing figurehead; he controlled the Hidden Mist by placing the Fourth Mizukage, Yagura, under mind-control; and he was the one responsible for the Nine-Tailed Fox's attack on the Hidden Leaf, which made Naruto both an orphan and a jinchuuriki.
And it has been revealed that the man behind Tobi is the real Madara Uchiha, with Obito carrying out his original plan.
The YuYu Hakusho manga reveals at the end that every villain Yusuke faces throughout the series is acting with the approval and, in some cases, the aid of King Enma, who wants to make himself look better by having major threats repeatedly stopped by Yusuke and allies (who work for him). The anime opted instead to end with another Tournament Arc, which was glossed over in the manga.
King Enma only brainwashed and released some Class-D demons in order to increase the number of crimes solved in the human world and present the demon world as a threat to justify the maintenance of a barrier and the spirit world's taking territory in the Demon World. He was most likely not behind Hiei, Kurama, and Gouki's theft of the sacred treasures, the Four Saint Beasts' plan, or Toguro or Sensui's falls into evil. While he might have been responsible for some of the demons getting free (Yusuke asks Kurama if any of the brainwashed demons — who were executed when they were recaptured — were ones he had caught and Kurama tells him it's best not to think about it), he's not responsible for what the major villains did. The "Tournament Arc" was in the manga, but they only showed the fights in the anime, and left out much of the action in the "epilogue" arc, including the barrier being removed, religious extremists taking over the Gates of Judgment, or Genkai passing away, instead concluding the anime at episode 112, the episode after the last battle.
In Yu-Gi-Oh! GX, the villain of the third season, Professor Viper, is revealed to be working for a Duel Monster spirit named Yubel. Later in Season 4, initial villain "Trueman" is revealed to be working for Yusuke Fujiwara...only for Yusuke to be revealed as a host for Nightshroud, the true villain.
Yu-Gi-Oh 5Ds has a series of these. The first true villains are the Dark Signers lead by Roman. The second season reveals that Roman was manipulated by Yliaster and the Three Nobles, who in turn work for Z-one. Furthermore, it is revealed Z-one was the commanding force for Paradox in the 10th anniversary movie.
Stellvia of the Universe does this very well with non-personified antagonists. The supernova (the Big Bad for the first half of the series) was caused by the crack in space, which is the antagonist for the second half.
InuYasha has Naraku, the puppeteer behind just about EVERY conflict in the show, past and present. At the end of the series, Naraku proves to have a man behind him as well — the Jewel of Four Souls itself.
Late in the Houshin Engi manga, it's revealed that Dakki is working for Jyoka, one of the First People who was sealed away for wanting to wipe out everything on Earth and make it into their old homeworld. Dakki agreed to help her in exchange for great power, but planned to take over Jyoka's body and use its power to rule the Earth.
In Gundam 00, who would've thought that Ribbons Almarck was manipulating Alejandro Corner?
Dragon Ball Z does this several times in a row in the manga and the anime. After Raditz is defeated Nappa and Vegeta are revealed to be the Saiyans behind the Saiyan. After they are defeated, Kaio mentions the "root" of the problem, which is shortly afterwards introduced as the Saiyans' (ex-)boss, Frieza.
Majin Buu had an odd version of this going for him. He was a childish weapon of destruction at first, but inside him was a psychotic weapon of destruction, and inside him was a Child of mass destruction.
Blood+ does this fairly often. In early episodes, Van Argeno is set up as the Big Bad; however, after about ten episodes, he's revealed to be working to Solomon. Later, Solomon is shown to actually be the lowest-ranking of five Chevaliers. Then, for a time, their progenitor Diva is expected to be the mastermind, but she turns out to be too crazy to be the leader. By the end, it's become apparent that Amshel is calling the shots, whereas Argeno — who was the first supposed Big Bad, remember — is reduced to cowering in fear and begging for his life. As a kind of a last hurrah, the final episode also implies that Nathan had been pulling the strings all along.
In Darker than Black, it looks like it's such a Mêlée à Trois that there can't possibly be a Big Bad. However, it turns out that The Syndicate, the dueling intelligence agencies, the Japanese police force, and PANDORA were all controlled by the same people. Evening Primrose was actually La Résistance, and other than their influence, all the conflict in the series had been due to the higher-ups pitting the Contractors against each other to keep them from finding out their genocidal plans.
In GaoGaiGar, the season 1 Big Bad Pasdar turns out to be a subordinate of one of the 31 Primevals, which are themselves fragments of the much more fearsome Z Master.
This is implied near the end of Fruits Basket, after Akito's Heel-Face Turn, the 'man' in question being the Sohma family elders, who criticize Akito for not emotionally destroying the members of the Zodiac..
Weiß Kreuz has layer after layer of this. In season 1, Reiji Takatori is the man behind criminal organizations like the Creeper gang and the Liott prostitution ring, and Essett is behind Takatori. In season 2, Mayumi Tsujii is behind Todou and S Class, and Epitaph (and by extension Essett again) is behind Tsujii. Rampant Chronic Backstabbing Disorder — particularly on the parts of Schwarz, who start out as one of the groups that Reijia Takatori is behind and end up backstabbing their way right out of Essett altogether — muddies the exact order in both cases.
Shishio is set up as the Big Bad of Rurouni Kenshin, but behind him is Enishi, the final villain of the series. Shishio has at his disposal an ultra-modern (for the setting) gunship, which he got through Enishi, who owns a fleet of them, and Enishi's Dragon/ Evil Genius hides among Shishio's group, pretending to be Dumb Muscle.
Dark in Asu no Yoichi! is introduced as a self-aware puppet serving the current Torikago clan leader who is set up to be the apparent Big Bad. When the leader is swayed by Yoichi's kind words, Dark reveals her true nature: she is the one who has been keeping the Torikago clan's hatred towards the Karasuma clan alive for generations. Dark turns against her supposed master, stating that she has no right to forgive the Karasuma clan after her ancestors devoted their entire lives to hating them.
In Pretty Cure All Stars DX 3, similar to the Sailor Moon example above it's revealed that the creature known as Black Hole was the source of all evil the girls face. It's kind of hard to figure out, though, if he meant the villains from the TV series itself (which wouldn't make sense as Suite Pretty Cure ♪ was going on at the time) or the villains from the various movies up to that point (whom he resurrected for this).
In Science Ninja Team Gatchaman, Berg Katse is presented as the face and leader of the Galactor. The viewer finds out long before the characters that Sosai X is the true power.
While he was a more traditional Big Bad in the manga, in the Trigun anime Knives Millions instead occupies this role, with his Dragon Legato doing most of the work until the very end.
The heroes in Warren Ellis's Nextwave: Agents of H.A.T.E., spend most of the series battling or evading Dirk Anger of the evil Beyond Corporation. Once they beat him, they face the Beyond Corporation's CEO, Number None... who is revealed to be a robot controlled by a baby M.O.D.O.K., who claims to be the Diabolical Mastermind behind it all... before being shot dead by Devil Dinosaur, the real lizard behind the man.
In Grant Morrison's New X-Men, John Sublime is the Man Behind the U-Men, the Weapon Plus Project, Kid Omega, and Xorn. About the only major villain that can't be traced back to him is Cassandra Nova.
In some of its last issues before being abruptly cancelled, The Incredibles seems to imply that the film's villain Syndrome may have possibly been doing business with or possibly working under the employ of Xerek (a character taken from early drafts of the film). Xerek's long in development Xanatos Gambit to discredit the supers further had two key components: An adapted use of the Omnidroid technology to create a bipedal giant mecha and the preserved brain of psychic superhero Everseer, who was one of the first victims of Syndrome's Omnidroid series, to act as a living psychic amplifier to enhance the abilities of another telepath/mind controller, Mezmerella.
Marvel's Loki does this so frequently he basically has this as his M.O., particularly in the Thor comics. The number of Thor Rogues Gallery that have nothing to do with him could be counted on one hand. Especially in the early days of The Mighty Thor just about every villain Thor ever faced was either created by or empowered by Loki in his attempts to kill Thor, sometimes as part of a multistep plan.
Downfall has an interesting one — although it appears at first glance that Unohana and her faction are the villains, subsequent perspectives given the readers have rendered that perspective uncertain. At best, that is only half the answer, and it is implied that some other force may be manipulating events.
Yoda Kenobi, author of the epic Star Wars fanfic series Legacy of the Sith loves this one. The villain of the first story is set up as Vagaari leader Goresh Tenziesh, but he turns out to be controlled by General Kol Renin, one of the leaders of the true Sith Empire. Then it's revealed that Renin is only an apprentice Sith. The real mastermind is his Master, Darth Malig. Now it's being foreshadowed that even Malig isn't the complete answer to the puzzle, though it's unknown if there's another villain controlling him or not.
The Legend of Spyro: A New Dawn has its first half with a Big Bad Ensemble consisting of Deadlock, Empress Tyrania, and Boss Kaze, though Deadlock is The Heavy of the three. The second half reveals that General Grendel, The Dragon to Deadlock, had been manipulating all three of them as part of his plan to gain an Artifact of Doom he can use to obtain the power of the Naga Spirit Of War and take revenge on the dragons for their banishment of the Naga thousands of years ago. In a twist, the readers know he's The Man Behind The Man at the halfway point, but the characters don't until after Deadlock is defeated and he successfully performs the ritual, giving him access to a civilization-destroying Eldritch Abomination.
During the first Story Arc of Jewel Of Darkness, Slade is this to Midnight — in this universe, she's the first Big Bad that the Titans face, as she tries to prove that she's a worthy apprentice to Slade. However, the Titans don't know this, viewing her as an independent villain; they don't learn of Slade's existence until the climax of the arc, when he shows up to rescue the defeated Midnight from the Titans.
Clash of the Elements: Part 2 reveals that Cackletta is responsible for pretty much all the villainous threats to Plit beforehand, up to and including Joe Dark and Tabuu.
The Stars Will Aid Their Escape: While the reader is aware from the beginning that Herald is the true Big Bad, the protagonists spend most of the story believing that his Unwitting Pawn Trixie is the main villain, until he reveals himself to them during the fight in Canterlot. And Herald himself is just a servant of the Old Ones, so they probably qualify as well.
Earth and Sky: To an extent, Diamond Tiara is this to the Flim-Flam brothers — while she may have lost control of them by the time the Pegalathon starts, she's still the one who sent them after Harmony Aeronautics in the first place, and is still covering for them the best she can. She also turns out to be the one who hired the LaFish brothers to attack the HA team during the race.
Erebos earns his position as Big Bad of the Ponies Of Olympus series by benefit of this trope. He was the one who turned Chrysalis into a changeling, sent her to invade during the Royal Wedding, and later sends her to infiltrate the Atlas Strongest Tournament; he was the one who corrupted Luna into Nightmare Moon; and Luna suspects that he was manipulating the conflict between the hippocampi and the dragons of the Scaly Back River Clan for his own benefit (though this hasn't been confirmed yet).
Burning Black: It's eventually discovered that Remy is in a "partnership" with the Pixies. However, the latter are clearly the superior party (despite what Remy might think) and are using Remy to further their own goal.
Friendship Is Aura: Lord Tartarus was the one who sent Chrysalis into Equestria in the first place, making him responsible for the incident at the wedding and her actions in-story.
Mr White, from James Bond. He first appears as the intermediary between Le Chiffre and the African warlords in Casino Royale, working on behalf of the shadowy terrorist organization Quantum. He only meets Bond once the film, when he kills Le Chiffre as punishment for his failures. Even after Bond captures him in Quantum of Solace, White escapes before he can give information, and also eludes Bond at a later point. It is suggested that White is one of the more mysterious leaders of Quantum, as he manipulates both the heroes and villains to his gain, repeatedly.
Inverted in the fourth The Fast and the Furious movie, where Dom and Paul try to find the identity of the one running the drug cartel by tracking their handler, but it turns out that the handler was the leader all along.
The sixth movie reveals that Big Bad Owen Shaw had the drug cartel within his pockets, along with the CIA, DEA and numerous terrorist organisations.
Rush Hour 2. This trope is discussed by Carter and Lee. Carter's theory of investigation is "Follow the Rich White Man." His belief is that behind every major crime there's a rich white man waiting for his cut. And he's right. In each movie, the Big Bad or one his associates is the rich white guy.
Professor Z's superior in Cars 2 is Sir Miles Axelrod, host of the World Grand Prix.
Referenced in Things Change, where Tony Mantegna passes off Don Ameche's character as powerful mobster who is "the man behind the man behind the man," getting lots of casino comps and explaining why no one has ever heard of him at the same time. Ameche is actually a simple shoe-shiner who is about to take the rap for a real mob boss. This scene was parodied in Swingers when Vince Vaugn's character jokingly makes the exact same claim about Jon Favreau at a casino.
Iron Man 3: The Mandarin turns out to be an actor used by Aldrich Killian to provide a face and distraction for the Extremis attacks.
In Now You See Me, you'd think that maybe Thaddeus is The Chessmaster behind the Four Horsemen, right? He's a former magician himself, and has a popular show that debunks magicians; what better disguise than to appear to be against them? Well, you're wrong. It's Dylan, the cop who was "chasing" them the entire time, and was actually using them for the ultimate purpose of framing Bradley.
Star Trek: Into Darkness plays with this trope in regards to Khan and Admiral Marcus. While the former is still the main villain long after the latter has left the picture, Marcus is still responsible for bringing Khan into the film in the first place and is a major figure in Section 31, a black ops group in Starfleet.
The Bourne Series: In The Bourne Identity, Ward Abbott was the mastermind behind Treadstone, and after eliminating Conklin, he's seen in a hearing laying down plans for the successor organization Blackbriar. It isn't until The Bourne Supremacy that he gets his comeuppance by Bourne.
In Watership Down, the antagonist rabbits from Efrafa corner the fierce fighting rabbit Bigwig, and are dismayed as he reveals that he is not the warren leader, but is defending the burrow at the orders of his chief — whom they assume must be even larger and stronger than he is. They're wrong — Hazel came by his authority and Bigwig's loyalty by being wiser, not stronger.
In The Hitchhiker's Guide to the Galaxy we meet Zaphod Beeblebrox, President of the Galaxy. We later find out that the purpose of the president of the galaxy is to distract the people from the real powers that be with his insane antics. In "The Restaurant at the End of the Universe", we finally meet the real ruler of the galaxy, who is a hermit who lives in a small hut near the sea with his cat. He likes fish. And he's not just the ruler of this galaxy but, it is implied, the entire universe — this galaxy is just where the Frogstar inhabitants placed him for safekeeping, but he receives other visitors from "far away, so far away" on a regular basis.
The definitive early science fiction series Lensman by E. E. “Doc” Smith, when read in publication order, is a classic example of this; one Man Behind The Man per book is revealed for three books running... The drug runners lead to the military force, which leads to the eternal force of darkness in the universe...
Glen Cook does this constantly in all his major works. Played straightest in Dread Empire where the titular empire, Shinsan, is controlled by its emperor who wins the succession struggle halfway through the series, O Shing. But he is really being controlled by a cabal of sorcerer-generals, the Tervola, who are actually being controlled by a conspiracy of 9 individuals at the highest places in society from across the globe/continent, who are actually being controlled by an immortal demigod (the Star Rider), who is being controlled by an ill defined higher, extra-dimensional power. That's where it stops, but probably not.
In Tolkien's story of the Fall of Númenor, Sauron allows himself to be captured by Ar-Pharazôn, King of Númenor, and soon goes from being prisoner of the King to channeling his power through the King.
Sauron's also heavily implied or outright stated to be the man behind Angmar, several barbarian invasions of Gondor, and at least one plague. He did a lot to weaken his enemies before revealing himself openly a few decades prior to LOTR.
The Black Council in the Dresden Files. Screw over and manipulate heroes and villains alike.
As of Cold Daysan entity called Nemesis is revealed to have possibly been the Man Behind The Man to the Black Council, and the Bigger Bad of the entire series. It is an Outsider that can infect people's minds, and is responsible for pretty much everything that's transpired so far, much of which Harry had previously attributed to the Black Council. The exact relationship between Nemesis and the Black Council remains unclear; it could be an organization that has been influenced by Nemesis, or they could be attempting to use it to further their own ends, or there may not even be a Black Council as such.
Book 1: Who's responsible for the serial-killing werewolf? Primarily Meg, who infected him with lycanthropy in a plan to unseat Carl as pack alpha, but in a strange example also Kitty herself, whose encouragement gave James the confidence to become a serial killer. An epic Nice Job Breaking It, Hero. The former was also responsible for Cormac's attack on Kitty.
Book 2: Four major villains all turn out to be connected: Senator Duke is the overt Big Bad, but he winds up in cahoots with Dr. Paul Fleming, Roger Stockton, and Leo, each of whom are pursuing their own agendas. Additionally, Leo, who seems to be playing the other three, is implied to be taking orders from the Department of Defense and/or someone else that even vampires are afraid of.
Book 3 gets tricky due to a Kudzu Plot. The curse on Kitty's cabin was cast by the Not-So-Harmless Villain Alice and Corrupt Hick Sheriff Marks, but the cattle mutilations were the work of a skinwalker that had been attracted by the evil energies of the curse, and the latter was also the sister of the werewolf that infected Ben. So ultimately, everything traces back to the skinwalker's grandfather, who also taught her what she knew. Who, after all that, proves to be an Anticlimax Boss since neither he nor the heroes can hurt each other, and killing him won't get the heroes what they want anyway.
Book 4: Who's the real bad guy in the vampiric civil war; Anti-Villain Arturo, or Rick? Neither. Mercedes was playing them both off each other for her own purposes.
Book 5: By this point, Kitty's getting Genre Savvy, so when Ben gets kidnapped, she suspects Balthasar. It turns out that Balthasar's show is a front for a cult led by his showgirl, who is the real vampire master of Las Vegas. However, in a Meta Twist, they had nothing to do with Ben's disappearance — that was the two-bit criminal the police suspected all along.
Book 6: The Band of Tiamat has to be behind the mysterious force stalking Kitty, right? Yes, but both they and Dom are pawns of Roman, who is implied to also have been pulling Leo's strings back in book two. Bonus points for being Chekhov's Gunman, having appeared previously as an unnamed bodyguard in Book 5 (Though that last might be a Retcon.)
Ruin wasn't controlling all of the other villains in Mistborn, but he was (directly or indirectly) the cause of most of their actions, as well as being the driving force behind a good portion of history and the entire prophecy of the Hero of Ages.
In the Warhammer 40,000Blood Angels novels, we learn that Dark Apostle Iskavan reports to Warmaster Garand, who in turn reports to Abbadon the Despoiler, while Inquisitor Stele's Chessmastery is still part of Malfallax's greater game.
Raymond E. Feist is in love with this one. Across the Riftwar Cycle, the first real villains (the first book was more Grey and Grey Morality) were the dark elves, who then turned out to be manipulated by the Pantathianpriests, who were in turn pawns for the Valheru. Later installments revealed that the Valheru themselves were being influenced by Nalar, and the final books revealed that he was just a Red Herring for the real Big Bad, the Dread. Among the side villains, the Dark God was manipulating the Dasati for centuries before taking its place as their ruler, and the demon legions currently trying to invade the mortal world are on the run from even worse demons back home. Both the Dark God and the aforementioned demons were eventually revealed as manifestations of the Dread as well.
Inverted in Goblet of Fire, where it's pretty obvious all along that the Man Behind the Man is going to be Voldemort, but who the Man himself is isn't clear. The most obvious suspect is Karkaroff, and others considered at various times include Snape, Viktor Krum, Ludo Bagman and Barty Crouch Sr.. The Man turns out to be who no-one expected - Barty Crouch Jr. (who was believed dead) disguised as Mad-Eye Moody.
In Death: This happens a few times. Immortal In Death reveals that Casto did the actual murdering. Betrayal In Death reveals that Naples hired Sylvester Yost in the first place. Divided In Death reveals that Sparrow, assistant director of Homeland Security Organization, put Blair Bissel up to murdering people.
In Steven Gould's novel Reflex, Davy and Millie Rice end up with a series of Men Behind Men at least three layers deep.
The Kingdom and the Crown has a council behind the council. The Great Sanhedrin is the official governing power in Jerusalem, but there is a smaller, more elite council where the real power lies. "The power behind the throne," as the Romans call it.
The Orions in the Star Trek Novel Verse. That dancing girl or prostitute is enslaved to a man who is in turn enslaved to a woman of the elite lineages, who in turn owes allegiance to a man who runs an entire branch of a crime syndicate, who is himself a servant of the woman who runs the entire syndicate from behind the throne...
In Andre Norton's Catseye, Troy faces Kyger for most of the work. After Kyger's murder, and some adventure, he's taken prisoner, to Dragur. In hindsight, Dragur's actual fascination with his marine animals means that the animal shop was a perfect cover for their dealings.
In the Shannara series, the Warlock Lord is the Big Bad of the first book (The Sword of Shannara) and its prequel (First King of Shannara), and is considered to have been the Biggest individual Bad in the setting's history. In The Wishsong of Shannara, some of his former minions learn sorcery themselves and turn into creatures called Mord Wraiths, who are collectively the new Big Bad. Except that's not how it works. The Warlock Lord was actually in the thrall of the Ildatch, an ancient, intelligent tome of Black Magic that wants people to use it, and will latch onto anyone with enough magical talent to make use of its spells, only to abandon them when they're defeated and/or someone better comes along. The Warlock Lord had it, and the Mord Wraiths took it after he died, and in both cases those who used the book became little more than husks that existed solely to use its powers. It's implied that the Ildatch has been doing this for milennia. Finally, when Wishsong's heroine Brin Ohmsford arrived to destroy it and the Mord Wraiths, it latched onto her and tried to turn her into a Dark Messiah, which would have worked if her brother hadn't snapped her out of it, at which point Brin used her magic to burn the Ildatch to ash. Good riddance.
In the Star Wars Expanded Universe, Onimi is revealed to have been manipulating Supreme Overlord Shimrra behind the scenes, and therefore is the one responsible for the Yuuzhan Vong's invasion of the galaxy.
Satan, to no one's surprise, is the man behind Nicolae Carpathia's rise to power, and the source of Nicolae's power (particularly when he indwells Nicolae at his "resurrection") in the Left Behind book series.
In Please Don't Tell My Parents I'm A Supervillain, because of their youth and the odd pattern of their attacks, the heroes believe that someone is directing The Inscrutable Machine, when in fact they're just attacking randomly. Played straight later when Spider blackmails them into helping her.
In one season, The Man Behind The Man is revealed around the middle of the "day", allowing Jack to spend the remaining episodes going after the real Big Bad.
In season 1, Dan and Rick (as well as Mandy and her assistant) were working for Ira Gaines, who himself was hired by the Drazens, while the Drazen brothers were working to bust their thought-dead father out of prison.
In season 2, Joe Wald was being manipulated by Nina Myers, who was working with Syed Ali, who was sold the nuclear device by Peter Kingsley, who himself was working under orders of Trepkos and Max. Max himself may have been the superior of the German woman talking to Nina at the end of season 1, making him the man behind the woman behind the woman.
In "The Game", Max was Peter Madsen's superior.
In season 3, Michael Amador and Marcus Alvers were working for Stephen Saunders.
And before we even knew about any of them, we originally thought the villains were the Salazars. While definitely not nice people, the Salazars were bluffing when they claimed to have the virus. They tried to buy it from Amador and ended up dead for it.
In season 4, Navi Araz was working for Habib Marwan.
In season 5, Anton Beresch was working for Ivan Erwich, who was working for Vladimir Bierko, who was working with Christopher Henderson, who was working for President Charles Logan.
In season 6, Abu Fayed's superior, General Habib, appears in one episode, but he was already captured by the time we learn about him. Fayed was also the attempted pawn of Dmitri Gredenko, however Gredenko died and Fayed seemed to reclaim his spot as antagonist, but died in the very next episode. Latter a different conspiracy emerged when the Chinese entered the picture, led by Cheng Zi, and they are revealed to be in cahoots with Jack's long lost father Phillip. Phillip and his son Graem were also Logan's co-conspirators in the previous conspiracy, or at least until they were seemingly retconned, as Logan recieved the full blame for it at the start of season 7.
In season 7, it's debatable whether Benjamin Juma's relations with Jonas Hodges count, as Hodges relationship is already stated in Redemption, and it can be interpreted as more of a Big Bad Duumvirate than Hodges being Juma's superior. On a far grander and less ambigious scale, even Hodges was merely a member of a large cabal headed by Alan Wilson, and Wilson was stated by Tony Almeida to have been The Man Behind The Man to President Evil Charles Logan.
In Season 8 Farhad Hassan and Samir Mehran were the Men Behind the assassination attempt on President Hassan. Meanwhile, Mehran was secretly supported by Russian Minister Mikhail Novakovich, who in turn answered to Russian President Yuri Suvarov who seemed to have undergone a Face-Heel Turn. They are later blackmailed into a new conspiracy, which involved both the US and Russian governments covering up the original conspiracy, signing the peace treaty, and attempting to kill Jack Bauer. The man behind it? None other than Former President Evil Charles Logan.
Alias: Throughout Season One, Sydney pursues a character that the show refers to as "The Man." Sure enough, the person they thought was The Man turns out to be The Dragon:
Sydney: What's going to happen to me?
Khasinau: You'll have to ask my boss.
Sydney: Your boss? I'm looking for The Man. Aren't you Alexander Khasinau?
Khasinau: Yes. Yes, but I am not The Man.
(The Man walks in)
Agents of S.H.I.E.L.D. does that a lot. In the beginning the bad guys are just various apparently unconnected minor conspiracies, such as the Centipede project, seemingly directed by Raina (aka "the girl in the flower dress") and Ian Quinn's evil corporation. It is later discovered that both Raina and Quinn spoiler:report to a mysterious employer known as the Clairvoyant. In Episode 16, SHIELD agents discovers "The Clairvoyant" in the person of Thomas Nash and kill him, but Nash himself says that name was given to him by someone else, and further analysis from Coulson makes it clear that Nash was at best a front and at worst just a decoy and another victim. The Big Bad now seems to be Victoria Hand, but may well be a front for yet another bigger bad.
American Idol: Nigel Lythgoe and Ken Warwick are this to the judges.
The Big Bad of Season 1's island/flashback storyline, Edward Fyers, turns out to be acting under orders from a mystery woman who seeks to profit from Fyers shooting down planes in Chinese airspace in order to crash their economy.
Burn Notice: In the episode "Dead to Rights", it is revealed that Larry was working for Anson — and not even Larry knew it, thanks to an elaborate plan.
Chuck: Has done this twice. Fulcrum was a part of the Ring, and these two, along with Volkoff Industries, were part of a conspiracy as clients of a firm led by Nicholas Quinn.
Day Break: The thugs targeting Hopper are commanded by the ominous "Man from the Quarry". We learn his name — Conrad Detweiler — only several episodes later. Then he is heard taking orders from somebody else — Tobias Booth. Who in one episode even executes him for allegedly leaking information to Hopper. But Booth is actually subordinate to Barry Colburn, who is the ultimate leader of the conspiracy. Hopper eventually learns the truth, but Colburn is actually so high up in the criminal chain that all his tracks are covered and Hopper can't do anything about him, so he remains a free man.
The final two episodes of the Ninth Doctor's run revealed that the Jagrafess supposedly masterminding Earth in "The Long Game" was actually a pawn of the Daleks.
Not to mention that the Jagrafess was the Man Behind the Man to the Editor in "The Long Game," making the Daleks the Man Behind the Man Behind the Man.
The earliest example of the Daleks being the Man Behind the Man Behind the Man was in Frontier in Space, in which case they were behind the Master, who was the Man Behind the Man to the Ogrons.
And Rassilon was the Man Behind the Man to the Master, having used the time vortex to give him the continuous sound of drums in his head, effectively torturing him into insanity.
Not the first time this was done with Rassilon. In "Zagreus" the Doctor and TARDIS have been infected by anti-time and turned into Zagreus. It is revealed these events have been set up by Rassilon for his plan to send Zagreus to destroy the Divergence. Then at the end of the Divergent Universe arc it is revealed Kro'ka, who was supposedly working for the Divergents, was working for Rassilon.
The races that formed the Alliance in "The Pandorica Opens/The Big Bang" were apparently manipulated by the Silents, who wouldn't even appear till next series.
In Doctor Who Magazine in "The Glorious Dead" it is revealed Cardinal Morningstar is Sato Katsura and he is working for the Master.
Falling Skies: For most of the first season, both the characters and the audience believe that the Skitters are the Big Bads. Then, near the end of the season, we meet the Overlords, and find out that the Skitters are just Slave Mooks.
Hawaii Five-O: Wo Fat, in both the 1968-80 original and the 2010 reboot—but much more prominently in the latter.
Heroes: Adam Monroe is the Man to the twelve founders of the Company.
In Plain Sight: Inverted Trope in one episode, where the mysterious contract killer "Lola" is a fabrication of her supposed underling, the real killer.
In Angel, it's made clear early on that corruptMega Corp. Wolfram And Hart is behind many lesser evils of LA, but who is behind Wolfram And Hart goes through several levels of reveal.
Season 1 reveals Holland Manners is behind the former face of W&H Lindsey McDonald.
Season 2 shows that W&H is behind the Corrupt Church that rules the dark dimension Pylea, and that true demons (the Senior Partners) are behind the mortal attorneys.
Season 4 has a different procession: The Beast (AKA Big Rubber Satan) is in front of Evil Cordelia, who is in front of (or rather, actually is) Eldritch Abomination Jasmine (who may be behind any number of other things, as well).
Firefly never got around to revealing much, but based on what we know about the show's planned Myth Arc, it appears that Blue Sun Corporation was meant to be behind most of The Alliance's evil tendencies.
Has done this several times. In the second season, it looked like Tom was the leader of the Others, until the finale when we learned of Benjamin Linus, who then revealed himself to be a pawn of Jacob, who is then murdered in the Season 5 finale, leaving the Man in Black to take the stage. And in all this mess, we still have Charles Widmore to worry about.
Averted Trope in that the Man in Black was "seen" in the very first episode and has been popping up throughout the series, seemingly in various dead guises. Also Jacob is not presented as an antagonist when he is finally revealed, and it is unclear just how much he has been ordering the Others around (though he probably could have stopped a lot of their worst actions) and hence how responsible he is for them, particularly since he spends a lot of time travelling.
The Prime-Time Premiere of the second season reveals that Lord Zedd was Rita's Big Boss, by imprisoning her in another dumpster but he was only the trope to the humans (viewers or in-universe). Zordon and Goldar (and it's implied the same to the other non-humans in the series) already knew Zedd was Rita's "lord and master" and was just too busy conquering other worlds prior to his debut, making him a Bigger Bad in their perspective.
While a vague allusion to a United Alliance of Evil in Zeo's premiere seems to imply a grander villain hierarchy than just Rita and Zedd, it isn't until the premiere of Power Rangers in Space that we learn Dark Specter had been the man behind the man for EVERY SEASON until then. Then Rita and Zedd's son tries to make himself into the man behind the various villain factions during the middle of Power Rangers Operation Overdrive. Doesn't last long but it was impressive for what is technically a nine-year-old.
Revolution: Throughout the first season, Randall Flynn seemed to have a mysterious agenda going on. Then in the first season finale, it turns out that he wanted to get the power back on so he could launch Intercontinental Ballistic Missiles at Atlanta and Philadelphia. Then he kills himself after his mission is accomplished. Not only that, but it turns out that he was working on behalf of the American government, which had stationed itself in Guantanamo Bay, Cuba for a long time. Now that Randall has accomplished his mission, the government is planning to go in and take back what's theirs.
Soap: when Danny decides he wants to leave The Mafia he tells his boss, who tells him he has to talk to the big boss of the Mafia - Mr. Lefkowitz.
Star Trek: Deep Space Nine: While it was not exactly a secret, Weyoun served as this with Damar in the last two seasons of . While Damar became the Leader of Cardassia after Dukat's capture, he served as nothing more than a puppet for Weyoun. Also from DS9 , Quark's mother Ishka becomes this for Grand Nagus Zek.
Star Trek: Enterprise: In Series 3, the Xindi race's attack on Earth made them the arc villains - however, as the ship searched for them in their home space, it happened across mysterious giant spheres warping reality, and then their architects, the extradimensional Sphere Builders. In the end it turned out the Xindi had been manipulated by the Sphere Builders into attacking Earth as part of a Batman Gambit to prevent them joining with humans against the Sphere Builders in the future, and the Sphere Builders were the real villains.
Twin Peaks: Although Agent Cooper encounters BOB in season 1 and Windom Earle in season 2, Windom Earle would be The Dragon, while BOB (who is never truly defeated) is the Big Bad.
White Collar: For the first season and a half, it seemed that Garrett Fowler was the man running things. Halfway through the second season, in "Point Blank", Fowler reveals he's being blackmailed by Neal's old boss, Vincent Adler.
Jovian Chronicles has the Venusian Bank doing this. It's implied that the majority of the CEGA is in fact in their pocket, if they don't own it wholesale.
One of the first adventure paths in role-playing, the G/D/Q series of 1st edition AD&D modules, was essentially this trope played out repeatedly: hill giants working for frost giants, frost giants for fire giants, all giants for drow, drow for Lolth. By the time you kill their demon-goddess, you're either crowing that you've bested the ''ultimate'' Man Behind The Man, or fed up and ready to play some one-shot adventures for a change.
In Paranoia, if the players ever investigate a really large-scale conspiracy and are about to get to the bottom of it, Friend Gamemaster is encouraged to introduce evidence that the culprits were being manipulated by someone else.
The secret societies in the Card GameIlluminati are structured so that you ultimately become one
Chakravartin the Creator in Asura's Wrath, when it is revealed that he is the one behind everything in the entire game. This is after you kill a ton of Jerkass Gods, a giant army of Eldritch Abominations, with a bigger one behind that whose heart happens to be the planet's core. All to "choose his heir".
In System Shock 2, it seems that Xerxes is the cause of all the problems on the ship. Then you run into The Many...
Its spiritual successor, BioShock, also does a masterful execution of it with Frank Fontaine. More specifically, he's the man behind you.
BioShock Infinite Continues this with the less villainous Lutece Twins who are unstuck in time able to manipulate everything seemingly to atone for messing with Booker and Anna as well as enabling Comstock to gain all his power.
Most of the Final Fantasy series follow the pattern of an initial antagonist (often a powerful and ambitious but relatively mundane Evil Empire or Corporation) which is rendered mostly irrelevant halfway through the game by the revelation of the main antagonist. Sometimes, as in the above two examples, the final battle reveals that this antagonist was also just a Dragon for the true Big Bad, usually a quasi-divine "source of all evil" in that world.
Final Fantasy II plays with this a little. When you defeat The Emperor, about 3/4 into the game, the game makes you think that Leon, who up until this point was serving the empire, is going to be your new Big Bad, but then we get a subversion when The Emperor comes back from hell to rule the world.
Final Fantasy IV (Final Fantasy 2 in the US) sends you after the evil Golbez. In the end, you discover not only was he being compelled to be evil from afar but that he also teams up with the main characters to defeat said evil from afar.
To take the Final Fantasy IV example further Golbez was actually the man behind King Baron near the beginning of the game. Making the real Big Bad The Man Behind The Man Behind The Man.
Several times, the main antagonist was set up as described above, or has even been on the losing end of a Man Behind the Man moment, only to take the reins from his supposed master. Final Fantasy VI was a hallmark in the series because Kefka, the Big Bad, appeared very early on and made appearances through the game. While he was serving an Emperor during his initial appearance, a later plot twist had him kill said leader and become a god.
Cult Classic Final Fantasy VII perhaps subverts this formula most successfully. Yes, the Shinra Corporation quickly proves to be less fatal than Sephiroth. And yes, Sephiroth couldn't have gotten to be what he was without them, Hojo and Jenova. But Sephiroth doesn't bother with manipulating Shinra, nor is Shinra delusional enough to attempt the same, and Shinra manages to stay a serious threat to the heroes right up to the end while Hojo and Jenova usually keep to the sidelines.
In Final Fantasy VIII, you spend the vast majority of the game chasing Edea; tragic back stories and conflicting emotions all come in to play about defeating your old mother-figure. But once you beat her, it turns out that your real enemy is a sorceress from the future who was controlling Edea. (Some fans criticize this as an Ass Pull to make the game longer, although it's actually foreshadowed as early as Edea's New Era Speech on disc 1.)
Final Fantasy IX starts with Queen Brahne trying to Take Over the World with weapons of magic destruction. Halfway through the game, her magic supplier, Kuja, kills her. Almost immediately it's revealed he's fighting against his former master, Garland, who is trying to kill everyone on Gaia and replace their souls with the souls of the people of Terra. Near the end of the game, Kuja kills Garland and tries to destroy all existence in a Suicidal Cosmic Temper Tantrum. The Final Boss is the Anthropomorphic Personification of Death, but he doesn't count as this trope because he wasn't controlling or manipulating anyone, but just shows up due to the Rule of Symbolism.
In Fatal Fury, Kain R. Heinlein is the Man Behind The Man to Grant.
Baten Kaitos Origin does this twice. After setting up Baelheit as the Big Bad for 95% at the game, a late game Reveal/Ass Pull reveals that he was in fact being manipulated by your mentor, Verus, who had previously shown no hints of evilness. And after you crush him, it turns out that he was in fact being manipulated by Wiseman, the dictator you supposedly destroyed 1000 years in the past.
In the previous game (and chronological successor), Geldoblame is set up as the Big Bad initially, until Melodia reveals that she was just waiting for him to get all of the parts of Malpercio into one place.
Subverted in Chrono Trigger, early in the game, your party learns the Big Bad caused an apocalyptic destruction of the world. Eventually, they find someone casting a dark ritual which is summoning the Big Bad. So, your party fights and defeats the summoner Magus, believing him to be The Man Behind The Man and finds out he was trying to summon Lavos to destroy him until your party disrupted the ritual
In the Rhythm GameSpace Channel 5, Ulala makes her way to the base of the Morolians, aliens who are using mind control rays to compel people to dance, only to discover that the Morolians themselves are being controlled by the real bad guy: Mr. Blank, the head of Space Channel 5, who orchestrated the whole invasion as a ratings stunt.
In Castlevania, there are a few small hints dropped that Death, who generally acts as Dracula's Dragon, may actually be this trope. There are also a few hints dropped that Death may obey a power beyond Dracula.
Castlevania: Chronicles of Sorrow games reveal that Chaos, the Ultimate Evil behind Castlevania itself, is this trope. This is the power that Death truly serves, though he seems to prefer Dracula being its host, given his hostile reaction to would-be usurpers. In Aria of Sorrow Chaos tries to force Dracula's reincarnation Soma to accept its power and become Dracula 2.0.
Galaxy Angel gameverse, anyone? The endless loops beginning with Eonia and emerging into the thing with Noa and the Val-Fasq escape my brain right now trying to explain them.
Phantasy Star enjoyed this quite a bit. In Phantasy Star 1, Big Bad Lassic is in fact a puppet of the demonic Dark Force, from whom he received all his power. In Phantasy Star 2, Mother Brain, a malfunctioning supercomputer, seems to be the Big Bad, only to be revealed as corrupted by the Earthmen, who were in turn corrupted by, surprise surprise, Dark Force.Phantasy Star 3 featured King Rulakir was Dark Force's most recent host and that the demon had been instigating the generations long feud between the two principal families. Phantasy Star IV seemed to break this cycle, revealing Dark Force early on, only for the party to destroy it three separate times. However, Dark Force itself is revealed as merely the most powerful fragments of the Profound Darkness that it had managed to slip through its seal once every thousand years, tasked with destroying the planets of the Algol system which formed the seal that kept the dark goddess imprisoned.
In the Xbox remake of Ninja Gaiden, Ryu goes after Doku, who stole the Dark Dragon Blade, only to find the sword in the hands of Doku's master, the Vigoorian Emperor. And after getting the sword back, the Dark Disciple (Murai) reveals that he instigated the theft in the first place. Admittedly, the Vigoorian Emperor doesn't actually report to the Dark Disciple, but it still counts somewhat.
Ninja Gaiden III on the NES does this too: Ryu finds out that Foster, the CIA agent from the first game, is creating super beings known as BIO-NOIDS and wants to kill him. Clancy, who was seemingly helping Ryu out, was actually using him to do his dirty work, and thus becomes the true enemy in the game, especially when Foster is killed for trying to chase Clancy into subspace.
Metal Gear Solid: The President, through Ocelot, manipulated Liquid Snake to his benefit.
Metal Gear Solid 2: The Patriot AIs manipulated everybody, including aforementioned president, aka Solidus Snake, as an experiment to prove themselves capable of manipulating the world.
Metal Gear Solid 3: The American branch of the defunct Philosophers succeed in pitting Naked Snake against his mentor and mother figure The Boss to obtain A MacGuffin Full of Money, which is used to create the Patriots in the future.
Metal Gear Solid 4: Due to everything above, the entire franchise's plot turns out to be a giant war proxy war between Naked Snake, aka Big Boss, against the Patriots, with Snake and Ocelot in this game being one giant smokescreen to distract the AIs from Big Boss' final move.
Metal Gear Solid: Peace Walker: Paz turns out to be behind the entire plot, as an agent of Cipher/The Patriots in an early attempt to trick Big Boss into developing a Metal Gear before discrediting his public image and thus force him to work for the Patriots.
Similarly, Baramos of Dragon Quest III is played up as the villain of the game, and you spend about 80% of the game — or what would feel like a normal full RPG of the time — hunting him down, only to have Baramos's boss, Zoma, call you out out of the blue after starting the victory party.
Halfway through Call of Duty 4, its revealed that the Al-Asad, the leader of the generic revolution in the nameless Middle Eastern country has actually been funded and supported by a mad Russian Ultranationalist named Imram Zakaev, who has visions of nuclear detonations dancing in his head.
Zakaev also shows up in "The Coup", handing Al-Asad a Desert Eagle which he uses to kill the president. At that point the player has no idea who he is and appears just as a creepy old one armed man in a trenchcoat. Because his appearance is so minor, most people don't notice him at all until they play the campaign again.
In Modern Warfare 3, it's revealed Makarov was the one who detonated the nuke.
Touhou likes to use this, in Perfect Cherry Blossom you have winter taking too long to go away, you soon discover it's not the Winter Youkai's fault, but the Ghost Princess, Yuyuko Saigyouji's doings. But, Yuyuko is being helped by Yukari, who allowed her to do her willings, and later enjoy a match with the main character.
In Imperishable Night, you freeze the night to find the one who stole the moon. You will encounter Eirin, thinking she's the culprit, but she's just helping her princess, Kaguya, who needs to escape from some noisy lunarians. Again, by the POV of Fujiwara no Mokou, she is attacked either by a team or another, but again, there's Kaguya behind it, convincing the team on a "trial of guts".
Super Smash Bros. Brawl takes this to ridiculous extents: Wario was being directed by Bowser and Ganondorf, who also manipulate the Ancient Minister (who also directs the R.O.B. Squad), the forefront of the Subspace Army, which is created by manipulating Mr. Game & Watch), but in turn are being given orders by Master Hand, who is being manipulated by some weird energy being that resembles "Tron" called Tabuu. Holy bejeezus.
Emo Teen Iska stops following you like a lapdog and starts stabbing at you in his One-Winged Angel form after beating Sultan Barbaross.
One of the endings of Drakengard has this occur. Throughout the game, we've become accustomed to thinking the Big Bad was the crazy high priestess of the Cult of the Watchers. When she's finally killed in the path to the fourth ending, the "Watchers" themselves show up. While it is left ambiguous if these are the true villains of the game, the sequel removes all doubt.
In Warhammer 40,000: Dawn of War, the campaign starts as an apparent defense against an Ork invasion. However, it is soon revealed that a Chaos force is having the Orks run interference. Then within the Chaos force, it becomes clear that Chaos Sorcerer Sindri Myr and not the "primary commander" Chaos Lord Bale is the one really pulling the strings, masterminding the operation to his own gain. Beyond that, in the final cutscene it's suggested that even Sindri was a pawn to the daemon locked in the Malectidum.
The Rival Schools series revolves around a number of student attacks among the various high schools in the area. Our heroes defeat those students responsible, only to find that they have been brainwashed by the faculty of Justice High. Upon defeating them, they discover that the true mastermind is the school's principal, Raizo. After they defeat him, they discover that he has been brainwashed by his nephew (and student body president) Hyo. And after defeating him, it is revealed that Hyo has been brainwashed by his father. Who is dead. Curses.
There's almost always someone behind King Dedede's attacks. And sometimes someone behind the one who is behind Dedede's attacks.
The first game in the Phoenix Wright: Ace Attorney series has Miles Edgeworth, the smug, arrogant "genius prosecutor" who will "do anything to get a guilty verdict." Then in the fourth case of the game, you're up against the devilish-sounding and looking Manfred von Karma, Edgeworth's mentor. It doesn't help that von Karma, also a perfectionist, tries to get the boy he took in since Edgeworth's father died found guilty for the sake of preserving his 40-year-long perfect record. Not only that, but the identity of the murderer in that case is deduced by Phoenix in court, but it's not until he he finds a letter in said culprit's shack that he discovers that it was von Karma who came up with the plan for the murder.
Ace Attorney Investigations: Miles Edgeworth has a large scale international smuggling ring, and throughout a large portion of the game, you see small areas of it, and solve crimes related to it. Eventually you find out that Calisto Yew not only ordered a hit job, murdered two men in cold blood, tried shooting the main protagonist dead, betrayed and back-stabbed her friends, but is also part of the smuggling ring AND ON TOP OF THAT also claims to be the Yatagarasu. Throughout a large portion of the game, you're lead to believe she's the big bad, and the person behind everything. Until it's eventually revealed that she's just a puppet who was being ordered around by the REAL big bad, the ringleader of the entire smuggling operation.
The Advance Wars series enjoys this one. In Advance Wars, Sturm was the Man behind Olaf and Clone Andy. In Dual Strike, Von Bolt was the Man behind Kindle and the Bolt Guard. And in Days Of Ruin, Caulder was the Man behind just about everybody.
In the Sega Genesis version of Golden Axe, Death Adder is hyped up to be the Big Bad, until you defeat him and realize he's been taking orders, and that you have one more level to go through. The true last boss turned out to be a recolor named Death Bringer.
Mass Effect:The first game's main villain, Saren Arterius, is actually mind-controlled by his ship, Sovereign, which itself is a Reaper intent on using him to wipe out all advanced organic life in the galaxy.
And in the sequel the Collectors are being controlled by Harbinger, another Reaper. Of course this time round Shepard and The Illusive Man are both Genre Savvy enough they guess that the Reapers are behind everything again right off the bat.
And the finale of the trilogy reveals the Reapers are just carrying out the mission given to them by the Catalyst.
And the Catalyst was originally the pawn of the Leviathan, until it betrayed them during a Zeroth Law Rebellion.
World of Warcraft uses this throughout all its major lore, almost every villain in the game that isn't an Old God or Sargeras is being controlled by one of those two. Speculation about the madness of Sargeras could potentially reveal a connection between him and the Old Gods as well.
Predator: Concrete Jungle starts off with you hunting street gangs before a coherent Big Bad, Hunter Borgia, is set up. However, while hunting him, you eventually stumble on the real Big Bad, the computer that controls Neonopolis, MOTHER, who is not actually an AI but his dear old mumsy Isabella Borgia, who has been kept alive through a combination of technology and the blood you spilt on her and Hunter back in 1930. Then she releases a wave of xenomorphs on you.
Warcraft III is an odd example. The Lich King turns out to be the man behind the Dreadlord Mal'ganis, who is also part of The Burning Legion, which turns out to be the man behind the Lich King, who later betrays his masters after they take over the control of the undead. So we effectively the Lich King being the man behind one of his masters for a while.
The final boss of Overlord is The Man Behind The Man. If that doesn't sound interesting then keep in mind you're the man he was behind in the first place.
The final boss (not counting the Bonus Dungeon) in Dark Cloud 2 is not Emperor Griffon, but the dark energy inside him made manifest: Dark Element.
Grodus, the main bad guy in Paper Mario: The Thousand-Year Door, tries to rule the world by reviving the Shadow Queen, who is an evil spirit sealed away for 1000 years. When Grodus summons her, she turns on him and defeats him with one measly attack before turning her attention to Mario. It turns out that Goldfish Poop Gang were her lackeys and manipulating the events... or rather the gang's leader was, since of the other two one is a moron and the other pulls a Heel-Face Turn. You'd wonder why the latter never mentions this to her new friends, but then again it really didn't make much difference to the party who, exactly, was trying to rule the world.
Guild Wars Nightfall reveals that the banished god Abaddon was behind most of the events of the Prophecies and Factions campaigns.
Jade Empire has two, with Death's Hand first appearing to be a bad guy acting on his own, and then revealing he has been acting on the Emperor's orders all along and the Emperor was the one who set up the death of the Water Dragon and the upsetting of the balance in the first place, and then once you defeat himyour kindly old Master Li wanders in, reveals that this was all part of his Evil Plan to get vengeance on his brother, and kills you, and it turns out that he is the final boss after all that.
In Ultimate Spider-Man, the man behind the man isn't the Final Boss. Venom is laid out as the main villain but you play as him. The big bads seem to be Silver Sable and Nick Fury. They send multiple villains after you but they're just lackeys. The real mastermind is Trask and he made Venom do all those bad things. His only power is money and military control. Venom later holds a grudge and goes after him when he's able to control the suit. Spiderman later goes to save him and fights Venom as the final boss, as well as another. Venom eats him and he deserves it.
In the Kingdom Hearts series, with a small handful of exceptions, all villains lead back to Xehanort. In Birth By Sleep we find out Master Xehanort is the past incarnation of Xehanort before he took over Terra's body, so ultimately every single thing wrong in the Kingdom Hearts universe is a direct or indirect result of Xehanort's actions. The only villain who doesn't seem to be under his control is Maleficent and her various allies, but they carry out their plans using Heartless. Guess who created the Heartless?
Legacy of Kain has The Men Behind The Men—the main antagonist for most of the series of Moebius, who is the controlling force behind the Sarafan and other vampire hunters, and is also a controlling force in the Circle of Nine. However, he's The Dragon to the Elder God, who is also the force that motivated the Ancients to war with the Hylden. Moebius' accomplice is Mortanius, the Big Bad of the first game until we find out he was acting under the possession of the Hylden Lord, who returns as the Big Bad of Blood Omen II where he leads the second incarnation of the Sarafan.
In the original Neoquest: on easy, the game ends after you defeat the Big Bad. On medium, you have to defeat the man behind the man after that. On hard you have to defeat not only the first two, but the man behind the man behind the man as well.
Oh, that's just the end of it. You first find out that Nametame was the one kidnapping all the characters you've been trying to rescue, but then it turns out he was just being manipulated by Adachi, who was the one who committed the first two murders that started the game. But then after you beat him, he gets taken over by a giant disco eyeball named Ameno-sagiri who claims to have done all this to "grant mankind its true desires." But THEN it turns out Izanami was behind it all, creating the Midnight Channel, the Shadows, and Ameno-sagiri, and giving the protagonist, Nametame, and Adachi their powers as part of her grand social experiment.
Nyarlathotep is the main baddie behind everything in both the original Persona and Persona 2
Persona 4 Arena: Shadow Labrys may have caused the P1 Grand Prix, but the unknown human referred to as Eerie Voice was the one who stole her and threw her into the TV. In turn, Eerie Voice is being influenced by the similarly obfuscated Malevolent Entity. Malevolent Entity even implies it was The Man Behind The Man in Persona 3 and Persona 4. Adding to this the implication that the Malevolent Entity is actually Nyarlathotep, the Persona series will get him as the ultimate villain responsible for absolutely everything.
Final Fantasy Tactics uses this trope a lot. The War of the Lions is orchestrated by the Church to seize power over Ivalice; the Church is being manipulated from within from Folmarv; Folmarv, in turn, is being used as a host by the Lucavi. In addition, it's also inverted: Dycedarg, Duke Larg's attendant, is ultimately responsible for much of what the Northern Sky does. However, as a big theme of the game is corruption and greed in the aristocracy, it doesn't come off as ridiculous.
This sort of thing in general is a common theme in the works of game designer Yasumi Matsuno.
In Pokémon Black and White, N is supposedly the boss of Team Plasma. However, it is revealed at the end that Ghetsis was pulling the strings the whole time.
In Pokémon Colosseum, Nascour is built up to be the Big Bad of the game. However, the true Big Bad is really Mayor Es Cade, or Evice, as he calls himself during The Reveal. This actually has a very sigificant moment of Foreshadowing in the beginning. Notice how Nascour casually walks out of Es Cade's house before you talk with him. And then the sequel reveals that Es Cade wasn't the true leader either
In Fire Emblem: Sacred Stones, Emperor Vigarde appears to be the Big Bad or the Evil Overlord, But he is in fact not even in control of his own actions, having died months prior to the first chapter of the game's events and was being animated by Lyon's magic. Lyon meanwhile, can either be overconfident that he is in control of the Demon King or is actually mercilessly possessed by the Demon King, depending on the story route chosen.
In Magi-Nation, Korg and Zet appear to have something to do with the Shadow Geyzers, but in fact it is revealed that someone named Morag is their master. But in fact, Agram is actually the teacher of Morag.
In Tales of Destiny II/Eternia, it is believed that Balir is in fact trying to bring about the Grand Fall, but it is revealed that Balir is actually long dead, and that his wife Shizel is carrying on in his footsteps. It is then later revealed that she is under the control of Nereid.
In Super Mario RPG, you're led to believe that the giant sword piercing Bowser's Castle is the Final Boss, Smithy. However, when you fight the sword, you learn that it is only Smithy's minion, Exxor, and that inside him is a Villain World where the real Smithy lives. Despite the original disguise, Smithy is still a Sequential Boss.
In Dungeon Siege 2, the Archmage turns out to not only be behind Valdis's actions, but also behind YOUR actions by disguising himself as Mr.Exposition.
In Destroy All Humans!! Path of the Furon, there is a long, confusing, Gambit Roulette example. The Master. Crypto believes his ememy is Curt Calvin, supposedly another Furon DNA gatherer. Then, after meeting the Master, Crypto believes his enemy is really Saxon, who supposedly used Calvin to try and destroy Crypto. It then turns out that Saxon was under the employ of Francodyne CEO Henri Crousteau. It is then revealed that Saxon and Crousteau were both part of Emperor Meningitis's operation to manufacture Synthetic DNA. Then after killing Meningitis, the Master appears and reveals that he was the actual conspirator all along, using all of them, including Crypto, in order to usurp the Furon throne.
The Conduit has one of these revealed in a voiceover after the game ends.
In the Sega Genesis game Shining Force almost every boss you fight, no matter how big of a bastard they were, turns out to have been innocent and only under the control of the real Big Bad, Darksol. It's really kind of irritating to have worked so hard to defeat someone only to have them go "What have I done? Forgive me, I was only under the control of Darksol, I'm actually good." before they die. Yeah, and we're supposed to forgive you after you killed more than half of the Shining Force?
Both Deus Ex games make liberal use of this trope. In the first, the NSF is working for/with the protagonist's brother, Paul Denton, who is in turn working with Tracer Tong and the Illuminati under Morgan Everett. On the other side, UNATCO is under the thumb of Walton Simons and FEMA, who are puppets of Majestic-12, which is in turn led by Bob Page. Interestingly, the player knows who the Big Bad is because he's right there in the opening cinematic. The fun in the plotline is seeing how it eventually connects to him. The sequel Deus Ex: Invisible War cranks it up a notch: The Order church is secretly being run by The Illuminati, and their mortal enemies the WTO are also under the control of the Illuminati, who use the conflict between the two as a cover for controlling the world economy. There's a nifty bit of foreshadowing in the "Coffee Wars" subplot, where the rival coffeehouses Peequod's and QueeQuegs are both under the control of a single corporation- which is in turn controlled by the Illuminati. Meanwhile, the Tarsus project is under the control of ApostleCorp, which in a strange case of Hijacked by Ganon is run by JC Denton, the protagonist from the first game. Damn.
In The Godfather: The Game, the Barzini Don is fingered as the one keeping the nearly-ruined Tattaglias alive and responsible for Sonny's death. In-game, when you die after having taken over a business but not the racket in the back, you will find that the business still counts as under enemy control and is still defended by them. It's even literal, as most rackets are located in backrooms of the legitimate businesses.
Roth in the second game.
Michael can be seen as this, since while both Aldo and Dominic are the nominal Dons, they're taking their cues from him.
In Luminous Arc 2, at first Master Mattias was build up to be a villain along with Fatima. However, later in the game, Bharva was revealed to be The Man Behind The Man and was responsible for the fire that killed Rina and Steiner's parents and give suggestions to started the Runic Engine research in order to kill all humans. Behind him is Mage Queen Elicia from 4000 years ago, whose research in life gives her immortality and created the Beast Fiends.
The same game has a straighter example with Shadow being The Man Behind The Man for Eggman.
Subverted in Sonic Generations. You fight Dr. Eggman twice in the game, both times end up with him getting kidnapped by the Time Eater. Then, when you get to the final boss, you expect to fight the aforementioned abductor. However, it is actually revealed that Eggman was behind the Time Eater after all. You proceed to become Super Sonics and smash his latest creation.
Guardians Crusade has multiple fakeouts that all hit at once, such as who the prophesied Hero (you're just babysitting), what Baby is as well as who the real villain is. But don't mistake the fake villain for a silly plot twist: before the reveals the Disc One Final Boss had set up cults in every city of the world, which are now launching an all-out assault and doing more side-quest related damage than the demon frolicking in the middle of the ocean is even bothering to do.
Hector, at first, seems to only be the Big Bad of the Dept Heaven game Riviera: The Promised Land, but supplemental materiel reveals that he had a hand in the entire series. He's the one who had Nessiah tortured and exiled, causing his madness and subsequently leading directly to the events of Yggdra Union, and he's the one who manipulated the events leading to Marietta's fall from grace in Knights in the Nightmare.
Baldur's Gate: So you came back Where It All Began and killed the leaders of the evil organisation that was pushing for the threat of war to gain money and power and was behind all the troubles in the Sword Coast? That might sound like it was the end, but in the game, you'll probably not think that. Sure enough, it turns out they were only pawns for Sarevok, their leader's adopted son, whose motives are more of the "seas of blood" and "A God Am I" sort. And so were you, if you actually did kill them; if not, he'll just frame you for it.
The Iron Throne in turn were the men behind Davaeorn, who was the man behind the Chill and Black Talon bandits, who were the men behind Mulahey and the kobolds in Nashkel. Oi.
Throne of Bhaal: The Five are clearly the enemies, leading their armies to destroy those who they think who stand in the way of their ascension. Only actually their leader is the apparent philanthropist Melissan, who also gives you many of your quests as a good guy.
In Xenogears, Ramsus is introduced as being the main antagonist of the story. It turns out that his unassuming girlfriend, Miang, is the real villain. Not only that, but she is essentially "god" in human form, and she has been manipulating world events for 10,000 years.
Its spiritual successor Xenosaga has a rare 'good guy' example. chaos was the man behind the man to none other than Jesus: he did the miracles, Jesus got the credit.
The Legend of Dragoon first starts off with Dart's girlfriend being captured and imprisoned. When he arrives at her place of capture he is quickly introduced to a man named Frugel, who is the cruel warden of Helena prison. After defeating him Dart learns that he in fact takes orders from Emperor Doel, who lives in the Black Castle of Kazas. Doel also is taking orders from a man named Lloyd, who is acting as The Dragon for Emperor Diaz. Emperor Diaz is revealed to actually be Dart's father, Zieg Feld, who plays the part of the main antagonist for the rest of the game up until the final boss, Melbu Frahma, who was posessing Zieg the entire time.
In Sam & Max: The Devil's Playhouse, it is revealed that the true mastermind of the events of the third season is not Skun-ka'pe, not Papierwaite, not Yog Soggoth, and not even Junior. It is Max's super-ego, the narrator of the game, who got tired waiting for Max to discover his cultured side (Max is all id).
Same in the first season, where the true villain is Hugh Bliss, who is actually a sentient colony of alien bacteria that feeds on happiness.
And in the second season, the true villain appears to be The Devil, but he is actually a pawn in the hands of the Soda Poppers, a trio of growth-stunted former child actors.
Tatanga, the main villain of Super Mario Land, is actually revealed to be working for Wario in the game's sequel. And the main reason why he kidnapped Princess Daisy in the first place? He did this just to distract Mario so Wario will succeed in his evil plans!
Age of Mythology has several levels of this. The initially presented villain is Kamos the pirate, who turns out to be working for the cyclops warlord Gargarensis. Gargarensis is getting divine backing from Poseidon, and they're both working to free their ultimate master the Titan Kronos, who if freed has promised to give Poseidon the power to defeat Zeus, and make Gargarensis immortal.
In Embric of Wulfhammer's Castle , the Awesome Fellowship's Arch-Enemy Lord Vecnathrax is actually being manipulated by Loni, who is taking advantage of his senility to pit him against the Fellowship for the artistic value of the struggles.
The end chapter of The Witcher reveals The Man Behind The Man, necessitating an Epilogue chapter to deal with him.
Mortal Kombat does this, more specifically in Mortal Kombat II. In the first game, Shang Tsung is hyped as the big bad, a deadly, powerful, long haired, evil sorcerer who has taken control of the shaolin tournament through unethical means, and corrupted it into chaos, ensuring that with 10 consecutive victories, he can take over Earthrealm. It's later revealed he's doing this for his boss, the emperor of Outworld, Shao Kahn, who the good guys eventually met when they're forced to continue a new tournament in Outworld itself.
It goes even behind that. In Mortal Kombat Deception, although foreshadowing had hinted at it in earlier games, we are faced with the resurrection and revival of Onaga, the Dragon King, former ruler of Outworld. The one Shao Kahn was formally an advisor to, and who he killed so he could take his throne.
Doesn't stop there. Shao Kahn and Onaga are both said to be manipulated by the One Being. The immortal omnipotent being that existed before the realms were created, that battled the Elder Gods before time. As he couldn't be defeated, the Elder Gods shattered his existence using a powerful weapon, and used it to create the realms before he could reform. The One Being is now essentially all reality, and his conscious exists within everyone. The only way for him to return is to merge the realms together, of which Shao Kahn and Onaga subconsciously try to do.
In The Reconstruction, Havan behind Skint. Subverted by the man in front of the man turning out to not have been a villain in the first place. The real Big Bad also has much shallower motives than the fake one, which may qualify as an additional subversion.
Dragon Age: Origins – Awakening reveals that the Architect, a sapient darkspawn trying to "free" his kind and give them free will, awakened Urthemiel, Big Bad of Origins, and caused the Fifth Blight. Unusually, this was accidental; the Architect is trying to stop the Blights, and inadvertently tainted Urthemiel while trying to "free" him. Nice job breaking it, antivillain.
In The Legend of Zelda: Skyward Sword, The Imprisoned/Demise is this for Lord Ghirahim. Not that Ghirahim keeps it a secret that he's not the one in charge. Demise is this for Ganon as well by way of the latter being an incarnation of the former's hatred.
In Dark Souls, Gwyndolin is the one secretly behind Gwynevere, with the Gwynevere you face actually being an illusion. Gwyndolin is using her to manipulate the Undead into linking the fire, so then he can ruling through her by proxy.
Kid Icarus: Uprising sets you up to fight Medusa, the Big Bad of the previous NES game. It turns out Medusa's resurrection was just a distraction courtesy of the true villain, Hades.
Super Robot Wars UX, Hazard from Tobikage is responsible for 90% of the trouble you have with humans in the game and then some. He manipulates the government and media, depicting your guys as terrorists, is arrested but breaks out of prison and somehow manages to become the supreme commander of the UN forces and nukes the Festum resulting in the events of the Fafner movies, when Sakomizu (Rean) attacks him, Mamoru (Fafner) protects the ship because it has nukes on it but then Hazard just shoots at both of them, hitting and killing just Mamoru. He gives Rouri (Rean) a nuke to drop on Tokyo, which in the end leads to Sakomizu's death. He fires off nukes again during the operation Azure II leading to Misao's (Fafner) death. He turns the Mazinkaiser SKL bad guys (humans) into unwilling suicide bombers and helps Mishima (Macross F) to brainwash the Vajra.
In Robopon, Circe apparently kicked the crap out of Knives in a Robopon battle at some point after he got his title as Master, rendering him mute and giving her the title.
Audience: has the white Darkky that curses Litho and manipulates Showtime in the cold open of the first episode.
Sluggy Freelance: Torg (the hero) himself becomes The Man Behind The Man to the wannabeDiabolical Mastermind Minion Master, while convincing the Minion Master that he's his minion. He's secretly using the Minion Master to obtain the technology to rescue his friends, and manipulating the Minion Master to take out other supervillains rather than do evil. Then the whole pattern gets more complicated with more serious villains getting involved, and more men hiding behind each other ensues.
For a 'Mastermind', he's easily manipulated; his own sister manipulates him as well, and they both get burned.
Dr. Schlock has usurped Prometheus as the Man behind Hereti Corp. Since it's a corporation full of evil characters, there's quite a few figures he can get behind.
We've now met the Evil Outsiders behind the Linear Guild - although in this case Sabine is the only one who knows about them.
General Tarquin and his friend Malack are the men behind several of the easy-come-easy-go kingdoms on the Western Continent. In the case of the Empire of Blood, at least, they're doing all the real ruling for the Empress, an unusually thick (in more ways than one) red dragon. But it's even deeper than that: Their four old adventuring buddies are behind the thrones of two other empires, using manipulation and war politics to ensure their anonymous power no matter who's nominally in charge - and the figurehead changes regularly.
Redcloak is this to Lord Xykon. He acts submissive and serves the role as Xykon's toady while actually manipulating him to his own ends. Or at least he thinks he is. It's strongly hinted that Xykon is aware of it and believes he is manipulating Redcloak, and he's certainly been on the ball about Redcloak (and family)'s plans in the past.
The Dark One is this to Redcloak (making him/it the man behind the man behind the man) — every action Redcloak takes is to fulfil the Dark One's Plans.
Complicatedly used in Homestuck. The Black Monarchs are the Big Bads at first, but their Dragon with an Agenda, Jack Noir, kills them and assumes the title. Later it's revealed that Vriska manipulated events so that Jack rose to power. And even later, Doc Scratch reveals he manipulated her all as part of his own plan to bring his boss, Lord English, into the universe. It's hinted however that the ultimate Big Bad may in fact be Lil' Cal.
El Goonish Shive: The Big Bad of the "New and Old Flames" arc turned out to be the short, hairy, quiet comic book geek, Dex. But it turns out he was under some kind of Mind Control. The main cast know it must have been an immortal due to the circumstances, but only the reader and maybe a couple of other characters know it was Pandora.
Spacetrawler: The protagonists initially believe Kuu-Drahc, Apex Speaker of the Galactic Organizational Body, to be the Big Bad. As it turns out, he's just taking orders from Qwahntoo, the guy who enslaved the Eebs and founded the Galactic Organizational Body in the first place.
Don Sebastiano, the Big Bad who rules Whateley Academy in the Whateley Universe, dropped hints for some time that Hekate, his 'queen', scared even him. Now we know that she was really behind the horrific act that gave Don Sebastiano his power base. BUT we also know there's someone behind her. Someone we've never seen except in a concealing cloak...
More recently there's been a story about a villain who became the Man Behind The Man by accident - basically bluffing a smallish gang and checking up on them later to discover they'd set up the international 'Master of the World Network', with thousands of pawns, all channelling money and information back to that one gang leader, who was more than happy to give it all to his 'Master'. Later on in the story this villain does a similar thing, except this time he actually does control it all.
Semi-invoked in Broken Saints: The two Chessmasters behind the Big Plan are presented as equal threats, only differing in that one stays more mysterious for longer than the other. Then, naturally, it turns out the more mysterious one, Lear, was just manipulating his more active partner Palmer, whom the heroes thought was the Big Bad. Lear betrays and murders Palmer, revealing himself to be the real Big Bad.
In Cult Of Personality, which takes place before Mann Vs. Machine, the then unknown Gray Mann is supporting oWn with funding, weapons, and prototypes of his robots in exchange for combat footage. Said combat footage would then be used to improve the AI of the robots and make them more closer to the mercenaries in terms of combat expertise and personality.
When former Big Bad Slade comes Back from the Dead on Teen Titans, it soon becomes apparent that someone or something is pulling his strings this time around, confirmed at the end of the episode "Birthmark" when he is shown kneeling to an unseen figure and calling it "master". It turns out to be Raven's demonic father, Trigon the Terrible.
A non-villainous version in SWAT Kats: It's pretty obvious that Deputy Mayor Callie Briggs is the one who really runs Megakat City, which is a good thing considering how incredibly incompetent Mayor Manx is.
In the first season of X-Men: Evolution, Magneto is this to Mystique, who is in turn the Man Behind the Man to the Brotherhood as far as the X-Men are concerned (though both the viewer and Xavier knew about her from the start, and the viewer knew Magneto was meddling from the end of the first episode). Later on, Apocalypse is the man behind Mesmero.
Twin Masters to High Roller in the second season of Hero 108.
Crooler to Cragger in LEGOLegends of Chima; Crooler is the truly evil one of them using rage-inducing pollen to control Cragger so she can use his newfound power as leader of the crocodile tribe for her own goals.