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- In Darker Than Black, nearly everyone works for The Syndicate, although most of them don't know it. Part of the point of this is to trick Contractors into wiping themselves out, as most of them work for various intelligence agencies in (seeming) opposition.
- In Death Note, following L's death, Light Yagami takes control of both the Japanese task force and his own Evil Plan to rule the world. He intended to let the task force be the losing side. It fails spectacularly.
- In Mobile Suit Gundam Wing, Zechs Merquise and Treize Khushrenada assume control of La Résistance and The Federation respectively and get into a giant, potentially apocalyptic war. While they seem to be bitter enemies, the anime strongly implies (and the manga outright states) that the whole thing is a Batman Gambit to bring peace by showing humanity just how terrible war really is.
- In Madlax, Enfant had been supplying and coordinating both sides of the Gatz-Sonikan civil war.
- In Nextwave, the 'wavers discover that their anti-terrorist agency H.A.T.E. is actually owned and run by the Beyond© Corporation, the very terrorists they're supposed to be fighting.
- In Secret Warriors, it turned out that HYDRA secretly owned S.H.I.E.L.D. Then it turned out that Nick Fury knew this all along, and was using it to manipulate HYDRA.
- In Sillage, the heroine lands on a planet locked in an eternal war against machines. The inhabitants would have died years ago had it not been for the regular deliveries of food and supplies in large containers, though nobody knows who sends them. As Nävis investigates, she eventually discovers the AI running the robots is also the one responsible for the supply drops, as ages ago it was a military AI (they're sentient in this universe), so bored by peace it basically started running a real-life RTS, giving its opponents food so as to keep the game going.
- In The League of Extraordinary Gentlemen, M turns out to be Moriarty. He was recruited by the government in order to help control the criminal underworld. He can't decide if he's a government agent who controls the criminals, a criminal who controls a government agency or both.
Films — Animation
- In Cars 2, Sir Miles Axelrod is hosting the World Grand Prix to promote his Allinol and is the shadowy leader of the Lemons. This is all part of a larger effort to discredit alternative fuels and encourage greater reliance on conventional petroleum sources.
Films — Live-Action
- In the 1987 Dragnet movie, Reverend Whirley is the head of P.A.G.A.N..
- The League of Extraordinary Gentlemen: The Phantom, the League's archnemesis, is also M, the British government representative who recruited the League to stop the Phantom. He was once known as Professor James Moriarty.
- In The Matrix Reloaded, it is revealed that the Machine intelligence known as The Architect designed the Matrix to periodically spit out a messiah figure to start a small revolt, and Neo is the sixth. The reason? Human free will adds just enough chaos to the system to prevent complete virtual management—but allow one human to restart the war, and the system remains stable. As the Architect puts it, "Your life is the sum of a remainder of an unbalanced equation inherent to the programming of the Matrix." In essence, the war is just another part of the operation of the power plant known as the Matrix.
- In the Star Wars prequel trilogy, Palpatine ends up in charge of both the Republic as Supreme Chancellor and the Separatists as Darth Sidious. As Chancellor, the conflict is his means of securing total and eternal power and destroying the Jedi Order. As Sidious, he (through his apprentice Count Dooku) provides the external threat used to justify his expansion of government power. Given he ran both sides of the conflict, this effectively means the outcome of the war was completely irrelevant, as no matter who won he'd rule the galaxy and wipe out the Jedi, the war itself was just a means to an end.
- In Wag the Dog, political advisors attempt to create an "artificial war"—and trick the public into thinking it's the real thing.
- In Police Academy 6, the crime boss turns out to be the mayor. As mayor, he knew about the city's light rail plans which would increase property values in the covered areas, while as a crime boss, he could use a crime wave to drop property values so he could buy the land cheap.
- The main plot of Batman Returns: The Penguin has his gang (to which he appears to have no connection whatsoever in the public's mind) commit random acts of violence throughout Gotham City in order to make the city's current mayor look weak, while simultaneously running for mayor himself and claiming he's the only one who can restore order (and, From a Certain Point of View, he's telling the truth!). One of his allies even refers to "the Gulf of Tonkin" and "the Reichstag fire", both real-life events that might suggest to naïve viewers that both were False Flag Operations, when in fact they genuinely happened and were only exploited afterward.
- The possibility of this trope is what prevents the ring from going to Gondor (or anywhere else but Mt. Doom) in The Lord of the Rings—since Sauron alone can control the ring, any faction opposing him and attempting to use the ring would inevitably be corrupted to the point where Sauron himself (as the ring is to some degree a physical extension of his will and personality) would be controlling both the forces of Mordor and the forces opposing Mordor.
- Random Factor series: a giant space war has been going on for years. Then stuff starts going wrong, and the main character manages to gain access to the sentient AI running his side's war effort... but finds that actually, the two sides are orchestrating the war pretty precisely. Oh, and the people actually fighting and dying are half-size test-tube clones, on half-size space ships. Saves money, that way.
- It's done in American Gods. While Mr. Wednesday rallies the Old Gods, his partner Loki is leading the New Gods as Mr. World.
- Illuminatus!: Hagbard Celine is the leader of both the Legion of Dynamic Discord and the Illuminati.
- In Nineteen Eighty-Four, the resistance turns out to be run by the central government. Furthermore, the three world governments seem to be encouraging a state of constant warfare among them in order to better control their own populations—it's quite possible and often theorized that they are all really ruled by the same group, although this is never directly spelled out.
- In Mercedes Lackey's Dragon Jousters series, it is discovered that both leaders of the warring nations (Fantasy Counterpart Cultures of Upper and Lower Ancient Egypt) are being manipulated by a corrupt Magician's Guild. The death-energies from the soldiers in battle are harnessed as sacrifices to fuel an immortality/youth spell.
- Tanya Huff's Confederation of Valor series has this as a reveal in the last book: A heretofore unknown shapeshifting alien race started an intergalactic war just to study how the different species would behave, like mice in a labyrinth.
- In Discworld, Lord Vetinari is not only aware that there are numerous secret societies and conspiracies trying to overthrow him or replace him, but according to Guards! Guards!, he's even founded a few of them.
- Part of The Reveal in G. K. Chesterton's novel The Man Who Was Thursday, used for Mind Screw and Everyone Is Jesus in Purgatory purposes.
- In the Doctor Who New Adventures novel Toy Soldiers, there's a war where it turns out that both sides are being run by the same supercomputer, which had set the whole thing up because it had heard somewhere that periods of conflict often produce flowerings of creativity.
- In the Fablehaven series, it turns out that the Sphinx is both the captain of the Knights of Dawn, dedicated to keeping the demon prison sealed, and the mastermind behind The Society of The Evening Star, who are trying to gain control of the means to open the prison.
- Ender's Game has Peter and Valentine Wiggin. They are genius children using primitive, pre-Internet Sock Puppets, Locke and Demosthenes respectively, to manipulate the major political thinkers through phoney debates; Demosthenes a warmongering demogogue, Locke a diplomacy-minded intellectual, and contrary to Peter or Valentine's actual beliefs. It's all an elaborate plan on Peter's part to formally establish himself as a great political mind, with influence and hopefully power, without the handicap of his age.
- Hardboiled Wonderland And The End Of The World has two opposing factions, the Calcutecs that are paid to guard information, and the Semiotecs that steal and sell it. It's heavily implied that both organizations might be in cahoots, though, as with many things in the book, it's never revealed.
- Milo Minderbender of Catch-22 pulls this off quite well in wartime, managing to profit tons of money by battling his own planes against each other and, infamously, bombing his own military unit and friends.
Live Action TV
- In Kamen Rider Wizard, the Big Bad Wiseman and the Big Good White Wizard turn out to be the same Stranger Behind the Mask. He also happens to be the father of the MysteriousWaif character.
- In 1999, WWF featured a long and convoluted storyline about The Undertaker and his Ministry Of Darkness attempting to seize control of the WWF from former bad guy Vince McMahon under the orders of a mysterious figure known only as "The Higher Power". This "Higher Power" turned out to be... Vince McMahon. The Ministry of Darkness then merged with The Corporation to become the Corporate Ministry, and about five months of storyline was thrown out the window.
- Several Warhammer Chaos gods are prone to this, especially Tzeentch (the god of magic, messing with fate and Gambit Roulette) and Zuvassin (a minor chaos god of spite and failure).
- In Warhammer 40,000, there's not only Tzeentch, but the Eldar, the C'tan Deceiver, and the Inquisition running around trying to keep multiple sides fighting each other. Although in the Eldar's case, it's to redirect an enemy towards another to prevent them from targeting the Eldar.
- Near Tyranid space, a lot of rebellions turn out to be caused by a Genestealer cult manipulating the upper echelons of two or more factions, turning them against each other until the entire planet is consumed by war, making it easy prey for the hive fleet.
- In one of the Paranoia supplements, it's revealed that Friend Computer actually founded all the secret societies, just to see what would happen.
- In the latest editions of the corebook, the Computer and the Ultraviolets rank the societies according to how dangerous they are. Those that are less dangerous are usually deeply infiltrated and influenced by, if not outright run by, the Computer and/or Ultraviolets (FCCCP being the prime example); some of them were created by the Computer to guide dissident impulses in these less dangerous directions. Other more extreme ones, like PURGE, are too dangerous for the Computer to control... but almost all have high ranking Ultraviolets at the helm (or close enough to make a grab for the wheel) already.
- Shadowrun supplement Dragons of the Sixth World. Ryumyo is in control of both the legitimate government of Hawaii (King Kamehameha IV) and the ALOHA terrorist group opposing it.
- This is somewhat the point of the game Imperial. Players buy stock in different 1900-era European nations and win by accumulating the most money on their investments, not by conquering one another. Sometimes the best move is to take majority control of two counties (meaning you get to take that nation's turn) and have them fight each other.
- In the Card Game Race For The Galaxy, with the "Rebels vs. Imperium" extension it is possible for the same player to control both the Rebel Alliance and vital parts of the Imperium government. And they should, because their sources of victory points overlap: Holding lots of Rebel military worlds.
- Ace Combat 5 The Belkan War: The Belkans are aggravating/running both sides of the war.
- The Administrator in Team Fortress 2. To quote from her character entry: "In a World... where a lot of guys dressed up in red fight a lot of guys dressed up in blue, it's telling that she dresses in purple."
- The recurring CEO/weapon merchant/villain in Rogue Galaxy attempts to do this with the two biggest nations around so that he can continue to profit.
- Crackdown: The Reveal at the end of the game is that the leader of The Agency, a superpowered law-enforcement agency for which you're an agent, was the reason the city turned into such a den of crime in the first place — he'd been supplying the gangs with weapons, transportation and intel for years, turning them from random punks into serious threats. Thus, he got an excuse to declare martial law and unleash the Agents on the city... exactly what the point was, though, is never explained.
- In Assassin's Creed I, Robert de Sable is secretly leading both the Crusaders and the Saracens, right under both King Richard's and Saladin's noses.
- In the backstory the Templars were behind both the Allies and the Axis during World War 2. Churchill, Hitler, Stalin, and FDR were all part of the Order.
- In Headhunter, the head of the criminal organization also turns out to be the one in charge of the Anti-Crime Network.
- It's hard to tell how many sides there are in Xenosaga due to a Gambit Pileup of impressive complexity, but Wilhelm is in charge of all but one of them—the party.
- Well, the party and Dmitri Yuriev. Wilhelm has accounted for his actions and doesn't see him as a real threat, but Yuriev isn't actually under his control. Ormus/U-TIC, Vector, Hyams Heavy Industries, and large parts of the Federation, on the other hand...
- Irving of Wild ARMs 2 is behind both ARMS and Odessa. The theory was that either the world unites behind ARMS to defeat Odessa and then the true Big Bad, or else Odessa conquers the world and deals with the problem themselves.
- In Tales of Symphonia, both the Desians and the Church of Martel are run by Mithos Yggdrasil and Cruxis, who want to keep the two worlds Sylvarant and Tethe'alla in a permanent struggle for mana in a misguided effort to prevent another of the Magitek wars that ended up killing Mithos' dead sister, the Church's namesake.
- Admiral Tolwyn in Wing Commander IV, indirectly. He claims to favor peace while the Black Lance forces under his command carry out a False Flag Operation to incriminate the Border Worlds.
- In Deus Ex: Invisible War, it turns out that the WTO and the Order are both being run by members of the Illuminati. The entire conflict between them is orchestrated by the respective leaders, who are working together.
- This is foreshadowed by the more light hearted reveal that the archrival Pequod's and Queequeg's coffee chains are owned by the same company.
- Xenogears is a subversion. Both sides in the initial Kislev/Aveh war are being orchestrated, through various puppets, by Krelian, but it later turns out that this war is a pure sideshow to the actual events of the storyline, where there are multiple top-level factions with their own puppets, along with a couple of genuinely independent groups.
- The Elder Scrolls III: Morrowind:
- If you join Great House Hlaalu, one of their last assignments will be to wrestle control of the Camonna Tong from Orvas Dren. If you then complete the Thieves' Guild storyline, you become their top dog, as well. Congratulations, you are now running both sides in a decades-long Mob War between two organized crime networks!
- In a case that causes some Gameplay and Story Segregation, you can do this for the Mages Guild and Great House Telvanni. Unfortunately, the game doesn't recognize that you may already be the leader of the opposing faction when giving you a quest that would harm that faction. For example, a House Telvanni quest asks you to get the Mages Guild monopoly on magical training lifted. Likewise, a Mages Guild quest has you root out a Telvanni spy in their midst. If you're in charge of House Telvanni, that spy technically works for you. And because both factions cater to magic-using characters, it is likely that you'll want to join both if playing as a Mage.
- In Red vs. Blue, both sides report to Vic at Red/Blue Command. The Red and Blue conflict is really just a fake war to give the Freelancers stages for combat trials.
- The alternate reality from You're A Rotten Dirty Bastard has Marvel and DC Comics owned by Linkara, who wants a faithful adaptation of Iron Man vs. Batman III.
- In Worm, Coil eventually accomplishes this; having successfully eliminated every villain in the city not clandestinely in his employ, he then stages a disaster which causes the local civilian government to be decapitated and the head of the Parahuman Response Taskforce to be discredited. He then replaces the head of the PRT in his civilian identity, putting him in charge of the city's superheroes.
- In Drowtales, it turns out that the mysterious Nidraa'chal leader who lead them against the ruling Sharen family is actually Snadhya'rune Vel'Sharen, the eldest daughter of the empress, and two of her sisters were in on the plot as well in order to get rid of their mother.
- In The Order of the Stick, Elan's father's adventuring party has arranged to rule the better part of a continent by doing this.
- Rocky and Bullwinkle: Boris Badenov did this in "Missouri Mish-Mash."
- The adaptation of The Partridge Family IN SPACE!: the family gets taken to play a gig on a planet called Texxas (the two X's are deliberate on the part of its supremely stereotyped founder; feels the real Texas is too small for his tastes). When they find the owner will not let them leave, they find some cattle rustlers and try to see if they can get them off the planet. Surprise! In order to make his Texxas even more Texas than Texas, the owner runs all the outlaw gangs as well. In short, the family has to find another way off.
- Look at old photos of Abraham Lincoln and Jefferson Davis, the two leaders in the American Civil War. It's obviously the same guy. He wears a big fake beard as "Lincoln" and a swoopy wig as "Davis", but the cheekbones and eyes are identical. Then there is the squirrel!◊.
- During the 2016 US Presidential Election, some conspiracy prone commentators wondered if Donald Trump was being deliberately outrageous in his comments to undermine fellow Republican candidates and turn voters on the fence towards Hilary Clinton (Trump having given to the Clintons in previous campaigns being a prime piece of evidence). It died down as the General Election neared and Trump was shown to be as aggressive and outrageous against Clinton as he had been against any Republican contender, though it did get a nod in some of his more political missteps. Ultimately, if this was the play, it Went Horribly Wrong. Though believers in the conspiracy theory still insist that Trump and Clinton were conspiring together, regardless of all evidence of both political incompatibility and personal animosity between them, with the premise being that a Trump presidency was an acceptable Plan B for them (or whatever shadowy cabal of lizard-men they were working for).
- Due to the way corporate ownership works, one or more shareholders can easily wind up on the boards of two rival corporations. There are laws meant to prevent abuse of these situations, but they've got enough exploitable curlicues that strange stuff happens nonetheless.
- During the medieval, renaissance, and early-modern periods, Europe was basically run by a few closely interrelated families. The monarch of one warring nation could easily be prominent in the line of succession for the other's throne.
- One example of exactly how closely related opposing sides could be shows up in World War I, where King George V of England and Kaiser Wilhelm II of Germany were first cousins (they had a set of grandparents in common). George was also the first cousin of Tsar Nicholas II of Russia through the OTHER set of grandparents. Wilhelm and Nicolas, though, were only third cousins (though Wilhelm was the first cousin of Nicholas' wife).
- More than one conflict was actually resolved by a "personal union," where the same person simply became the ruler of both states. Most famously in the English-speaking world, Queen Elizabeth I ended the off-and-on war between England and Scotland by giving the English throne to King James VI of Scotland (who afterward was also James I of England). Since James was Elizabeth's cousin and she had no children and no living siblings, nor were there any living heirs to her siblings, he had one of the strongest claims to the English throne even if she hadn't named him her heir, but doing so removed all doubt. Sometimes a personal union would eventually lead to a permanent merger of the states involved, as was the case when England and Scotland became the Kingdom of Great Britain, but more often the situation was temporary.
- Another famous example: During the Reformation, Charles, soon to be named Holy Roman Emperor, inherited three separate kingdoms (plus additional dukedoms and provinces) from three separate dynasties in rapid succession to possess for a time the world's largest empire. He was Charles I, Charles II, Charles III, Charles IV, or Charles V, depending on which part of his empire he was visiting at the time.
- Yet another example from the Reformation Era. The French Wars of Religion were ended when the Protestant leader, Henry of Navarre, formally converted to Catholicism and became King Henry IV, with the condition that the Protestants were granted various rights and privileges in return (e.g. the right to maintain fortified towns).