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A conflict is going on. It might be a shooting war or just a fierce rivalry; it might be only important to some of the characters or important to nearly everyone in the setting. However, it turns out that while the subordinates on opposite sides feel very strongly about it, the leadership on either sides aren't enemies. They might even be the same person! Normally you'd expect someone in that position to attempt to defuse the conflict. But they don't, they encourage it, not because of Honor Before Reason, but because it is to their political advantage to keep the conflict going for the moment.
Spoiler Alert: Due to the nature of this trope, the mere listing of a work as an example could be a spoiler. While contributors are encouraged to hide spoilers where appropriate, reader beware.
Anime and Manga
- 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 Madlax, Enfant had been supplying and coordinating both sides of the Gatz-Sonikan civil war.
- In 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 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 Marvel Comics, it turned out that HYDRA secretly owned S.H.I.E.L.D.
- In Sillage, the heroine lands on a planet locked in 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 Navis 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 Star Wars prequel trilogy, Senator Palpatine ends up in charge of both the republic as Supreme Chancellor and its enemies as Darth Sidious. As chancellor, the conflict is useful to him politically, so he encourages it.
- In Wag the Dog, political advisors attempt to create an "artificial war" — and trick the public into thinking it's the real thing.
- 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 totally virtual management; 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 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.
- In the 1987 Dragnet movie, Reverend Whirley is the head of P.A.G.A.N..
- 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, many have theorized that the three world governments are encouraging a state of constant warfare among them in order to better control their own populations.
- In Mercedes Lackey's Dragon Jouster series, it is discovered that both leaders of the warring nations (expys 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 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, it has been said (in Men At Arms, I think) that a lot of the conspirations against Vetinari are run by Vetinari himself.
- 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.
- Hard-Boiled 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.
- 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 were 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).
- Ace Combat 5: The Belkans are aggravating/running both sides of the war.
- 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). 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.
- The Announcer 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, 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 and Hitler were both part of the Order.
- In Headhunter, the head of the criminal organisation 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 BigBad, 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 Little 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.
- 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.
- In Red vs. Blue, both sides report to Vic at Red/Blue Command.
- 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 Drowtales, it turns out that the mysterious Nidraa'chal leader is actually Snadhya'rune Vel'Sharen, and two of her sisters were in on the plot as well in order to get rid of their mother.
- In 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."
- 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!.
- 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.
- 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 of Scotland.