Secret War

The Marvel Comics Crisis Crossover can be found at Secret Wars.

A war that is kept secret from the public at large. The involved parties may or may not be unknown to Muggles as well, but the central concept of the trope is that the conflict itself is somehow hidden, covert or underground. Basic fodder for Conspiracy Theories and naturally fiction in general.

In trope-speak, a war that is concealed behind a Masquerade. Compare Great Offscreen War, where the war in question is kept from the audience.

Anime and Manga

 * Itsuki Koizumi implies multiple times that a particularly big and violent one is revolving around Haruhi Suzumiya in the titular series.
 * Iriya is also implied to be involved in one in Iriya no Sora, UFO no Natsu.
 * The ancient struggle between Denizens and Flame Haze in Shakugan no Shana. The Masquerade is remarkably easy to keep up when everyone can erase people from existence and pseudo-stop time.
 * The fights between the witches and the magical girls in Puella Magi Madoka Magica are a secret, meaning that the Magical Girl doing the fighting ends up isolated and friendless.

Comic Books

 * Marvel Comics' Secret War. Possibly Secret Wars too.
 * But not Secret Wars II.
 * The war with the Dire Wraiths starts out this way in ROM Spaceknight.
 * The Swedish cyberpunk comic De osynliga kriget turns out to be about a war fought with nanotech robots - destroying factories and infrastructure by making buildings fall down. To the public, that's just sloppy building practices that are part of their already Crapsack World.

Fan Fiction

 * Fittingly enough, a Secret War is what a 40k fanfiction called Secret War is all about.

Film
"Blade: You better wake up. The world you live in is just a sugar-coated topping! There is another world beneath it - the real world. And if you wanna survive it, you better learn to *pull the trigger!*"
 * The war between vampires and lycans in the Underworld series.
 * Partly thanks to the Cleaners, a group made up of elite human soldiers and headed by . Their job is to work behind the scenes to clean up the mess the immortals leave behind.
 * Also, the war between vampires and one very angry half-vampire in Blade


 * The Resistance of Zion vs. the Machines inside The Matrix.
 * The central conflict in Cats and Dogs.
 * In Hellboy, it's mentioned in passing that World War II was simply the public front of the Occult War, which only came to an end with Adolf Hitler's real death in 1958.

Literature
"If won, it would only be written of in the secret histories. If lost, there would be no more histories, secret or otherwise."
 * The long conflict between the Dark and the Light in The Dark Is Rising series.
 * Harry Potter: The war between the wizards.
 * The war between the Old and New Gods in American Gods.
 * The Star Trek Expanded Universe retcons the Eugenics Wars into a secret war, in an attempt to maintain Plausible Deniability after they didn't happen on schedule.
 * The war between in the first Empire From the Ashes book, which has been going on since the dawn of human civilization. By the end of the book, it has become very, very not secret—people don't know what the hell is going on, but they sure can see the mayhem.
 * Fyodor Berezin's The Lunar Option describes battles on the Moon between the American astronauts and the Soviet cosmonauts during the 60s, after the discovery of an alien artifact. Obviously, no one in the general public is aware of this.
 * Several of these in The Dresden Files, primarily among them the war between the White Council of Wizards and the Vampire Courts. There's also an even more secret war known as the Oblivion War, whereby a secret brotherhood known as the Venatori wage a conflict in order to eliminate all knowledge of certain monstrous entities, as knowledge of them possessed by mortals connects the entities to the real world.
 * The various Weird Wars in the Diogenes Club stories by Kim Newman. Every so often an evil Great Enchanter arises, and it's the Club's job to put him down again.


 * The war against the Yeerks in Animorphs. Until everything gets blown wide open in the end of the series.

Live Action TV

 * In Stargate SG-1 the US is involved in an interstellar war, and doesn't even tell the heads of other nations at first, never mind the world at large.
 * The original Star Trek episode "Assignment: Earth" was a Backdoor Pilot for a series that would've revolved around Gary Seven's secret battles with aliens. Fittingly, Seven was a protagonist in the Expanded Universe material mentioned in this page's Literature folder.
 * This has at times been proposed as an explanation for why the Eugenics Wars that supposedly happened at the end of the 20th Century don't exist—they did happen, just in secret.
 * Get Smart has CONTROL vs KAOS.
 * A number of the UNIT stories in Doctor Who work this way, particularly in the classic series.
 * Star Trek: Enterprise, the temporal war.
 * In the War of the Worlds series, only a handful of military, intelligence and science personnel know about the alien invasion coming out of dormancy. In the second series, the new aliens appear more human and are able to operate openly, since it's become such a Crapsack World that to most people they're indistinguishable from the corrupt corporations and organized crime.
 * Alphas has the fight between the alpha terrorist organization Red Flag and the Department of Defense and their own alpha team.

Tabletop RPG
"At the end of each faction turn, the GM should translate the turn’s events into a few lines of rumor or news that can be related to the PCs. A successful attack by the Lawyers of the Bright Dawn Society on the Perihelion government’s Union Toughs might be reported as “Neohuman rights activists on Perihelion applaud the election of Parminder Smith to the leadership of the government-sponsored Transit Workers Union. Miss Smith is a strong supporter of neohuman research and legal emancipation.”"
 * Warhammer 40,000: The Holy Inquisition Of Mankind fights a constant war against the forces of the alien, the mutant and the heretic. Civilians or even military forces who might have been exposed to the evil simply by knowing about it are executed, even if it's an entire planet. Of course, even the secret war is a front for what really happens, with Inquisitors fighting an even more secret war against each other.
 * Old World of Darkness is rife with secret war, going down between virtually every species of supernatural being, between different factions within the same species, and between supernaturals in general and those few groups of mortals who have been clued in to their existence.
 * Nephilim. The eons old combat between the title characters and the secret societies hunting them.
 * Call of Cthulhu (tabletop game) supplement Glozel Est Authentique, adventure "Secrets of the Kremlin''. The Nodens Brotherhood has long opposed a cult that worships Shub-Niggurath.
 * Bureau 13, AKA Stalking the Night Fantastic. The title Bureau fights against supernatural monsters.
 * Chill. S.A.V.E. (Societas Albae Viae Eterniata AKA The Eternal Society of the White Way) does battle with supernatural creatures from The Unknown.
 * Feng Shui has a secret war that spans at least four different junctures in time, along with the Netherworld that connects these junctures, each with their own different factions vying for the power to remake human history in their image.
 * The game Conspiracy X also has a secret war involving reptilian aliens and other weirdness.
 * The Shadowrun universe has rival Mega Corps waging a covert war against each other, with the titular Shadowrunners being the deniable assets that the corps call upon to do their dirty work.
 * GURPS Black Ops. The PCs all work for "The Company", a secret organization with the twin objectives of 1) Kill all the aliens/psis/monsters trying to take over and 2) Don't let anyone outside The Company find out about the aliens/psis/monsters trying to take over.
 * The Infinite Worlds default setting has the two factions of Centrum and the Infinity Patrol who oppose each other at every turn and vie for control and influence on low-tech worlds, all while trying not to be detected by the natives of that timeline and expose their own existence.
 * Cthulhu Tech gets crazy with the strength of their Extra-Strength Masquerade. The shadow war between the Eldritch Society and the Chrysalis Corporation taking place within the arcologies and suburbs of the NEG-controlled areas is one thing, and the Chrysalis Corporation are very good at keeping things under wraps and discrediting or eating anyone who knows too much and might actually expose anything (plus, they have the leverage to have the government censor Dhohanoid-related reporting to prevent public panic). However, not only are Eldritch Abomination cults are alive and well, but one has formed a military force that has conquered China, under wraps, and the fact that the last Aeon War is still going on and the Migou are attacking again . And the NEG can recruit people to fight on the China front without them knowing a thing about the war until they're already in too deep to back out.
 * Stars Without Number faction dynamics has most attacks and actions not involving Force type (i.e. military) assets work like this.

Video Games

 * In the Assassin's Creed series, there is an ongoing, secret war between the Assassins and the Templars, which has been waged since the beginning of the human species, ever since
 * The actual term is used in the section of The Secret World's website that deals with the three world-spanning conspiracies that are fighting against each other and the encroaching darkness that's threatening Earth. Preventing The End of the World as We Know It seems to be the only thing that the Templar, Illuminati and The Dragon agree on.
 * The war between the Forgotten and Abaddon's forces in Guild Wars: Nightfall qualifies. The Forgotten have spent the last thousand years fighting a slowly-losing war to keep Abaddon and his followers bound in the Realm of Torment. As of present, they maintain only scattered outposts in either dimension.
 * The Order of Whispers was founded to pursue such conflicts. They have watched over Palawa Joko's tomb, kept the existence of Abaddon and his demons from public knowledge, and a century before the game even interrogated and imprisoned a Titan.

Western Animation

 * In Avatar: The Last Airbender, the war is secret to the Earth King only. The Dai Li took pains to make sure it stayed that way to keep the people of Ba Sing Se from going into a panic and to limit the capital's involvement with the war that would screw up their way of living.
 * Its hinted that while the Earth King is kept from knowing to make him a puppet, that many of the rest of the citizens don't know either. Brainwashing and control of information keep knowledge down, and constant fear makes those who do know too afraid to talk.

Real Life

 * Real Life: CIA vs. KGB, CIA vs. Al-Qaeda, etc. The public only knows a very little about what really goes on behind the scenes.
 * During the Vietnam War the CIA had a whole lot of things going on, including the Phoenix Program (a program of infiltration, capture, terrorism, and assassination).
 * The Radical Religious Right is convinced that Christianity is waging a 'spiritual war' against the Devil/Satan. Of course, since the non-Christian religions are played off as the design of Satan/the Devil, this invariably extends to mean that all religions that are not their particular brand of Radical Christianity are automatically their enemy.
 * As well as atheists and the non-religious in general. This is particularly interesting in that in theory there's a secret war going on that involves every single living human being whether they know it or not.
 * "Secret" bombing campaigns. Governments usually (great, that's a porthole to hell) don't about it, but that doesn't mean that it's as publicized as a ground invasion.