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- Fullmetal Alchemist has an incredibly sinister government conspiracy that goes all the way back to the destruction of the ancient city of Xerxes.
- The Union in Str.A.In.: Strategic Armored Infantry, although the Black Box of their evil research was so secret that, five hundred years later, no one in the military had any idea where exactly Strains and Mimics came from. No one except the Defector from Decadence, that is. And they wonder why he snaps and starts trying to kill them.
- Giant Robo: The Day The Earth Stood Still has the miraculous Shizuma Drive, which ushers in the Third Energy Revolution and a new golden age for all mankind. Trouble is the first, hasty test of the Shizuma Drive wipes out an entire country in the Tragedy of Bashtarle, killing uncounted millions of people
- Actually, the real dark secret is that The revered Dr. Shizuma who is credited with the drive actually caused the destruction of Bashtarille by performing the final experiment against the advice and counsel of Dr. Franken Von Vogler, who was presumed lost in the accident — and who was blamed for the disaster. This comes back to bite EVERYONE on the ass.
- The Lost One Hundred Years within the One Piece universe is kept secret by the paranoid World Government. Any attempt to learn the lost language to decipher the secrets of the poneglyphs left behind by the long-forgotten civilization (i.e. something close to OUR civilization) that preceded the World Government will result in the immediate death of the researcher and anyone remotely connected with them as well as the obliteration of their research to the point of bombing an entire island into rubble!
- They destroyed an island for the crime of learning the language that could be used to read ancient texts that might possibly lead them to the truth of what happened during that time period.
- SEELE in Neon Genesis Evangelion is running a thousand-year old Ancient Conspiracy. Not only have they influenced humanity's advancement towards their Assimilation Plot but part of this influence was intentionally causing a global catastrophe (the awakening of Adam in the Antarctic which led to the melting of the polar ice caps and global sea levels rising and destroying all coastal settlements, this plus the resulting wars ending with a death toll of three billion) but covering it up as an asteroid impact. Oh, and the Captured Super-Entity they worship and want to use for said Assimilation Plot? A sentient terraforming device of alien origin (although they might not realize it themselves, the "sacred" Dead Sea Scrolls are actually an instruction manual misinterpreted as religious text). And the kicker: not only the Assimilation Plot will be what is essentially The End of the World as We Know It, SEELE's leadership of humanity from behind the scenes subtly influenced society in such a way that no one is 100% sane anymore and global birth rates are dropping rapidly so either they successfully pull out Instrumentality or humanity will die out in a few generations.
- The Alliance from Serenity had buried the fact that some time ago, they had accidentally killed 99.9% of the population of Miranda with a chemical meant to calm their violent urges, and turned the rest into the horrifically violent cannibal monsters that would become known to the rest of the Verse as the Reavers.
- In the Alternate History film, Fatherland, where Nazi Germany won World War II, a few people begin to investigate to the various "undesirable" populations who mysteriously disappeared. Of course this means they uncover the Final Solution's death camps.
- In MIB, it's revealed that not only do aliens live among us, but most modern inventions were actually gifts from alien civilizations, not human creations. Earth is repeatedly in cosmic peril and almost everyone on Earth remains in blissful ignorance.
K: There's always an Arquillian Battle Cruiser, or a Corillian Death Ray, or an intergalactic plague that is about to wipe out all life on this miserable little planet, and the only way these people can get on with their happy lives is that they do not know about it.
- The Wheel of Time has two.
- The Seanchan Empire can attribute its thousand-year history of prosperous expansion to enslaving feared and persecuted magic channelers as children, effectively making them extremely powerful, living tools that can be assigned and taken away by the higher-ups. No one realizes that the Phlebotinum for control only works when the controller has hidden potential to become a channeler. Controllers who learn this go into a pretty crippling state of denial in most cases, if not begging to be made slaves themselves.
- Likewise with the Aiel, which is a society made up entirely of Proud Warrior Race Guy practicing Honor Before Reason. It devastates them to learn that their ancestors were originally pacifists who turned away from their beliefs and failed in their mission to help the Aes Sedai in their task of transporting artifacts to safety. Once this is revealed to the general populace, about one in three are taken by "the bleakness": putting down their weapons and just walking off into the desert. Another faction, the Shaido, take up arms against the one who told them this, Rand al'Thor, in denial.
- In Scott Westerfeld's Succession series, the Risen Empire (a collection of 80 inhabited planets) is ruled by the Risen Emperor, who invented immortality in the form of a symbiote that attaches to corpses and brings them back to life. Of course, it turns out that this only works for 500 years or so, instead of true immortality. Needless to say, things get ugly.
- There's also the Humans in Zhan's The Conquerors Trilogy, who are widely feared for having a superweapon capable of irradiating entire fleets. It turned out to be based on a well-spun accident involving a solar flare.
- The Colonial Defense Forces in John Scalzi's Old Man's War has vat-grown supersoldiers where the basic DNA used as a template comes from volunteers who die before they can have their consciousness transferred to one of the normal engineered bodies, which they use as special ops forces.
- Borogravia in Monstrous Regiment. Turns out the Duchess who supposedly runs the country has been dead for years, their patron deity Nuggan has dwindled to nothing due to lack of belief, and approximately a third of the top military leaders, if not the entire army, is composed of women disguised as men.
- Nazi Germany in the book Fatherland. Unlike the film, the book leaves it very ambiguous whether the Dark Secret actually gets revealed.
- The Human Empire from Yulia Latynina's Inhuman is bloated and evil; a great deal of this is explicit, but corruption often turns out to run even deeper than initially thought. Better yet, a veteran of its foundation eventually explained to his great grand-son, one of the protagonists, that it used to be less corrupt and more monstrously evil back then, because that really was the only way to save humanity from the intelligent, rapidly-breeding, rapidly-growing, omnivorous Ttakas. That biological weapons were used is public knowledge; that the The Virus behind the rampant Assassins in Space-like terrorist organisation was originally created in the First Emperor's labs ran by the aforementioned veterans in order to brainwash human super soldiers into fighting with the reckless abandon required, along with some lesser things, is not quite as well known.
- This is very nearly the entire story of Ursula K. Le Guin's tale The Ones Who Walk Away From Omelas.
- Basically, it goes like this: She starts out describing a utopia. Then she decides that the readers won't believe in it, and starts trying to add things to change that... but none of them work until she settles on all the happiness and inspiration in the society relying on one horribly abused child. Right around then is when it solidifies into a little crystal of horror.
- Pretty much the entire point of the Green-Sky Trilogy by Zilpha Keatley Snyder, where the secret is that children were not taught about Earth's historical capacity for violence, the knowledge being kept by a select few, and anyone who disagreed with this policy got trapped below ground.
- In The Obsidian Trilogy, Armethalieh's mages get their magic from farming it from talismans they force the population to wear and exchange on a monthly basis, from humans who can't practice magic but still have a little of it within them. They also insist on having a society without change in order to prevent demon invasion, which they also don't mention.
- It's been noted in-universe neither of these secrets seems actually worth keeping; their citizenry wouldn't mind what's happening, it would reassure their neighbors and their system's breaking down entirely because nobody knows why they're really doing things and thus mismanage the few necessary changes. At the same time, Armethalieh is very openly doing some nasty things which have given it a dark and ugly reputation - and worse, by people who can be trusted to do these for the wrong reasons so not even they need be let in on it. The whole thing's a study in societal erosion, not at all natural.
- In Holly Lisle's Matrin novels, the Hars Ticlarim's source of magic is the slaves they keep below ground.
- In the Myst novels, the Terahnee appear to have a utopian world where automation and mechanical power means no one has to work. In reality, they're enslaving entire universes' worth of people to provide this "automation".
- Admittedly The Empire of Star Wars has the fairly simple dark secret of being run by an Emperor who does not actually have anyone else's best interests in mind, and this secret isn't all that secret. Throughout the Star Wars Expanded Universe there are Imperials who realize that they take issue with the Empire's methods and the things it has done to maintain itself. Most of them promptly join the Rebellion.
- The public are largely unaware that he is actually a Sith Lord, however; and, of course, they don't seem much aware of the fact that the Clone Wars were engineered by him because Despotism Justifies the Means, or that the Jedi were framed, etc. The Rebellion did its best to get word out about the numerous crimes of the Empire, but most citizens believed it to be Rebel propaganda.
- The five stormtroopers in Allegiance go through a Heel Realization and see that the Empire they joined to serve is vastly more callous, xenophobic, and outright uncaring about the lives of citizens than they had ever imagined. Realizing this contributes to them sort-of-accidentally killing an officer who took one of them to task for refusing to shoot unarmed civilians, and then they go on the run. In the same book we see that the Emperor's personal agent, Mara Jade, is fully aware of what people say about Palpatine. She just doesn't believe any of it, even if she's got a faint, repressed undercurrent of doubt.
- Mara Jade is introduced in The Thrawn Trilogy and her entire Character Arc for that story is basically one long Heel Realization about just how evil the man she had been serving really was. She always knew he wasn't a nice intergalactic dictator, but she was still haunted by his last command to avenge his death by killing Luke Skywalker; its only when she finds out that Vader was the killer, and the reason she was to kill Luke Skywalker was that he was actually Vader's son and thus it was a spiteful Revenge by Proxy, that she started to realize just how horrible he was, helped by her finding out that Luke himself was a pretty cool guy and The Empire she had been serving caused a lot more damage than she knew.
- The planet Necropolis in Galaxy of Fear has a weird subversion of this trope. They have a story that would make a great Dark Secret and a reason for why zombies are occasionally seen on the planet - a witch lived there hundreds of years ago, the Necropolitans murdered her son, she cursed them with zombies - but it's part of local mythology, and the locals cheerfully tell it to visitors. Maybe this really happened, maybe it didn't. The reason zombies are seen on Necropolis is totally innocuous, or it was until a Mad Scientist moved in - the local wildlife includes boneworms, which make fresh corpses spasm and sometimes outright move.
- Vorkosigan Saga: This is a peculiar case where it is the viewpoint society that is this. The dark secret is that the previous Emperor deliberately lost a war in order to assassinate his son Prince Serg in the process, because that was considered the Lesser of Two Evils compared with letting him come to the throne. Yes, Prince Serg really was that bad.
- All of Safehold was founded with the dark secret that the religion that underpins every country on the planet is a Path of Inspiration founded out of a combination of technophobia and megalomania on behalf of its central figures. Several figures have been kept out of the loop because if they found out the truth it would shatter their entire world view.
Live Action TV
- In the Doctor Who episode "The Beast Below", England, Wales and Northern Ireland (Scotland as mentioned in the episode built their own ship) are being carried through space on a star whale which they torture to control the speed - they know they can't justify their actions, but they're afraid that freeing the whale will destroy the ship. Thank goodness for Amy Pond, really. There's also the fact that they feed anyone who finds out the truth and disagrees with it to the whale. Or simply someone who doesn't do his homework. Luckily, the whale won't eat children.
- In the "Long Game", The Ninth Doctor takes Rose and Adam to a news space station called Satellite 5, in the year 200,000 - the era of the Fourth Great and Bountiful Human Empire. However, the Doctor notes that progress is relatively slow, or simply ground to a halt with most of humanity being docile. Then he discovers why - The Fourth Great and Bountiful Human Empire is not a human empire at all, or at least not human-led, and humanity is secretly being controlled by a monstrous alien known as the Jagrafess by controlling information. The Doctor and Rose would appear a century later with Jack Harkness to learn of the Jagrafess' own masters: The Daleks.
- Combining this with Path of Inspiration, the League of 20,000 Planets in Lexx was a theocracy headed by the Divine Order that supposedly brought order to the Light Universe and protected it from the chaos of the Dark Zone. His Divine Shadow ruled the League for thousands of years, and successfully indoctrinated humanity to fanatically worship him over generations. The dark secret of the League was that His Shadow was actually the essence of the last survivor of the Insect Civilization, a race of giant insects that fought and "lost" a genocidal war against humanity. The League's true purpose was to make humanity wholely enslaved to the Insect's desires, to the point that the entire population of the League of 20,000 willingly fed themselves to the Insect at the end of the first season. His Shadow reveals all of this to the crew of the Lexx, gloating over the way he used humans to defeat themselves.
- Hades in the folk opera Hadestown tells his Underworld subjects that he's keeping them safe from an enemy that doesn't actually exist.
- The Imperium in Warhammer 40,000 has gobs and gobs of this. Most of it self-delusional as well.
- The man they revere as their Emperor is a semi-conscious anti-theist hooked up to a life support machine which runs on the power of the thousands of psyker souls it eats daily, for a start. Even better: the religious canon that establishes him as God Emperor? It was written by one of the Primarchs who fell to Chaos. Specifically Lorgar, who fell to Chaos because while the Emperor didn't want anyone worshipping him, there were other deities in the Warp who would very much welcome believers...
- The ruling caste of the Tau Empire use mind control to inspire absolute loyalty in their subjects and hold their empire together. It's also very heavily implied that a piece of technology they gave to a vassal-species to enable direct mind-to-mind communication enabled them to extend said mind control over said species. Said ruling caste were also genetically engineered by the Eldar using the pheremone glands of a Q'orl Hive Queen and inserted into Tau society for their own ends.
- The Adeptus Mechanicus who keep all of the technology running worship a being known as the Omnissiah. In the overwhelming majority of cases this is another aspect of the Emperor, but around 1% worship the most powerful of the star-eating abominations known as the C'tan, the Void Dragon, which is currently asleep under the surface of Mars. And to make matters worse still, it is the 1% who are actually correct.
- Ironically, it was the Emperor himself who imprisoned the Void Dragon on Mars during the Middle Ages, as part of a Batman Gambit that would allow the foundation of the Adeptus Mechanicus (whom he needed to conquer the galaxy) thousands of years down the line.
- Most of the domains of Ravenloft are this trope. In some cases, their political rulers are actually darklords; in others, a Path of Inspiration has taken hold of the populace; in yet others, their societies are completely infiltrated by shapechangers, mind-controllers, sociopathic mad scientists/wizards, undead, or other malign forces. Or all of the above.
- The fact that the entire game-setting is a construct built by the Dark Powers, via dubious methods and for unknown purposes, also qualifies.
- Our whole world in KULT. Only our prison wardens know about it, and hunt those humans who know, or are coming close to it.
- SLA Industries has a Universe With a Dark Secret. Anyone who finds out The Truth either gets hunted down and killed, or ceases to exist on their own. The Truth is that the universe arose from the imagination of a psychic from our world, and they died before it was finished. A lot of the weirdnesses of the SLA universe come from attempts to 'patch over' the gaps. The was only revealed in the game's writers' bible, not in any of the sourcebooks (so far).
- Solaris in Xenogears. Of course, we know they're kind of evil from the outset, but the reasons of their existence and the sheer scale of their crimes are pretty incredible and known only by very, very few, and most citizens in particular are blissfully ignorant.
- Final Fantasy VII's Shin-Ra corporation holds an arguably exclusive secret; the Mako they use to make everyone's lives better is actually an extract of the life force of the planet.
- It's not exactly a secret in-game, it's just that most of the population doesn't care because either their lives are too comfortable or they are too miserable and desperate for it to matter. Of those who do care, only a handful are willing to actually stand up to the Shin-Ra army and try to do something about it.
- In Chrono Trigger, the highly magical floating continent of Zeal has a dark secret —- while they used to draw limited power from the renewable Sunstone, the new (nearly unlimited power source) for all of its magic comes from Lavos
- In Grandia II, Roan finds out that his people are the game's equivalent of Satan-worshipers, and decides they might as well be the best damned Satan-worshipers they can be, despite their end goal of killing him.
- In Mega Man Zero, unknown to the human residents of Neo Arcadia, their utopia comes at a price: the retirement of their fellow (innocent) Reploid citizens, courtesy of their supposedly messianic leader, Copy-X.
- The Jade Empire. Rain only falls because the Emperor and his family mortally wounded but did not kill the Water Dragon. As she is a goddess, if she is not killed she will simply live on, never reincarnating. Oh, and Emperor Sun Hai should have died a long time ago but is using the power of the Water Dragon to keep himself alive. Oh, and this was all caused by the emperor's brother, Sun Li, who's basically planning to bring about a perfect totalitarian state.
- In Mass Effect, unbeknownst to everyone, the Protheans did not build the Citadel or the Mass Relays before their mysterious disappearance 50,000 years ago. Both are in fact millions of years old and were originally constructed by the Reapers, as a means to direct all life in the Galaxy along the technological lines they desired, before they returned to cull all advanced civilisations every 50,000 years.
- In Mass Effect 3, it is revealed that the asari didn't become galactic top dog by being wisest and smartest and being gifted with natural mind powers. After encountering the salarians, the two races founded the Citadel Council. One of the highest laws of Citadel Space is that all artifacts of Prothean technology have to be shared with everyone to be studied by the top scientists of all races. Stealing or not revealing any discovery of artifacts is punished very severely and has huge diplomatic and political repercussions. However, the asari never revealed that they had a fully working database beacon on their homeworld for thousands of years, which made them the first species to rediscover the Mass Relays long before anyone else and was almost certainly the basis for genetic engineering that that led to their extremely unusual biology.
- The UPEO in the Japanese original Ace Combat 3: Electrosphere, secretly controlled by the two big corporations. Although, UPEO is more of a "UN-mandated global military with a dark secret" than any sort of empire.
- Starcraft II the Terran Dominion, Mengsk dark secret on sending the Zerg to attack Tarsonis, and his willingness to eliminate anyone who gets in his way. Also the Dominion (or at least some faction within it) has been secretly been creating a Zerg hybrid.
- Escape Velocity Nova: The rest of known space already knows one of the Federation's dark secrets, but since the rest of known space consists of a) a icy planet only inhabited because there's profit in the fur of one of the native species, b) an Empire of warrior houses the Federation is already at war with, c) an isolationist Higher-Tech Civilization already unfairly biased against the Earth-based Federation, d) a Rebellion triggered by some Federation citizens finding out the other dark secret (and then not being able to convince the public of it), that's doesn't really make things worse. It would probably be bad for Federation morale and internal stability if it came out that the Vell-os actually still are enslaved rather than voluntarily serving the Federation, though. The other dark secret the Federation has is that the Bureau have effectively usurped control, destroying the Federation's claim to be The Federation.
- The Sith Empire in Star Wars: The Old Republic hides an even darker secret than in the original movies, even though the vast majority of its citizens sees it as a more organized and less blatantly corrupt version of the Republic. Sure, there is rampant social Darwinism mired in outright racism, and they are ruled by a clique of insane Force-users who constantly murder each other and innocent bystanders for power and profit, but at least the social ladder makes sure the capable get all the way to the top, and the Emperor, while not benevolent, has a good enough grip on the other Sith and is far enough from the common folk for them to respect him in earnest. Well, in fact, the Sith Emperor doesn't give a flying crap about the Empire he founded, the Sith he nominally rules, and the rest of the petty state matters. The whole Empire thing got started to create enough docile population for him to kickstart a Dark Side of the Force ritual that would ultimately consume all life in the Galaxy Far, Far Away and elevate him to immortality and omnipotence. The only reason why he hasn't succeeded yet was the efforts of the two Knights of the Old Republic, Revan and the Exile, and now it's mainly up to the Hero of Tython (the Jedi Knight class character in SWTOR) to stop him for good, while the Empire remains by and large blissfully unaware of all this. It gets worse in the latest expansion Knights of the Fallen Empire. Not only does he not care for the Sith Empire at all, not only was he just using it as fuel for his ritual, but he was also secretly building another Empire, the Zakuul Eternal Empire, at the same time, on the other side of the galaxy. This is the reason why the Emperor had a tendency to remain silent for centuries at a time: his attention was focused on Zakuul via his avatar there, Emperor Valkorion.
- Veracia, largest and (at least until recently) most powerful nation in the world of Errant Story, is pretty much founded on this trope.
- Some of the most famous Slender Man stories, beginning with Seeking Truth, have stated or at least implied that the United States government is well aware of the Slender Man, and that there is an entire branch of agents dedicated essentially to being damage control and keeping anyone from revealing his existence, simultaneously killing, unpersoning or simply screwing over anyone attempting to reveal him... or, ultimately, destroy him.
- Until the 60s and 70s, Charles De Gaulle promoted what historians now call "the myth of the Resistance" i.e. that "France had liberated itself" and the Resistance was a widely popular event. While it did exist almost from the beginning of France's surrender, La Résistance was always a minority. Most of the French people accepted occupation out of indifference, stunned by defeat and apathy. The segment of the population who were Les Collaborateurs, were in fact numerically superior to La Résistance. The most famous example is Milice, pro-Nazi paramilitaries and the French police who participated in The Holocaust. This "myth" cracked in the 60s and 70s, and played a role in the May '68 Protests.
- War crimes committed by Japan during the Second World War are still taboo in today's Japan. A few official references still exist to it being a fight against Western imperialism. The people they conquered are not happy with that portrayal.
- This is true about nearly any and every country with a history of imperialism that wants to promote national pride in the present day. Some argue that this is especially bad in and/or hypocritical in the case of imperialism done by putatively democratic nations. Conquerers and Kings make no bones about them taking over other nations. The idea of "benign" empire, i.e. conquest disguised as civilizing missions was developed by Parliamentary Britain and Republican France to justify why, despite supporting principles of sovereignty at home, they chose to deny it to people in colonies abroad. The same applies to the USSR's empire, which occupied Poland and much of Eastern Europe.
- The corruption and violence of the French colonial empire was a big taboo in French society until its collapse. To some extent that taboo persists today. Many French today still do not know that one of the worst famines in history happened in Algeria after France conquered it. And likewise their schenanigans in Indo China and Vietnam. Indeed, it's likely that the Vietnam War could have been avoided entirely if France committed itself to decolonization after the war. Instead they persisted in holding on to both Vietnam and Algeria only to lose both amid bloody violence, mass repression and terrorism engendered in reaction to French hegemony.
- The United States is absolutely not an Empire, except for that time they conquered Mexico (which Ulysses B. Grant himself admitted was little more than land grabbing), or that time they conquered the Philippines in the Spanish American War, or that time they established several client states and dictators across Latin America and the Middle East.
- The British can't quite get away with saying that they weren't an empire. Instead much ink is spilled in Parliament and conservative press and literature about how the English were more benevolent than the other Empires, and how much worse things would have been if they hadn't conquered these nations. A counterfactual presented as a defense, often in the vein of invoking Benevolent Alien Invasion and What the Romans Have Done for Us! Never mind such blunders of diplomacy as the Sykes-Picot Agreement, the Irish Troubles, the Arab-Israeli conflict and the Partition of India, all of them consequences of British policies and whose consequences still persist to this day.
- In the Soviet Union, the existence of the Molotov-Ribbentrop Pact with Nazi Germany was vigorously denied by the Communist authorities until 1989. Likewise, the 1940 massacre of Polish officers in Katyn was vigorously denied as being a Soviet atrocity, the blame being laid on Nazi Germany between the massacre's discovery in 1943 and the opening of Soviet records in 1990, following the USSR's collapse.
- The People's Republic of China takes the official stance that it has never done anything bad to its people, though it is alone stating this. Most egregious would be the millions who died in the famines of The Second Five-Year Economic Plan/'Great Leap Forward'note , followed by the popular delusion and murderous mob-violence of The Cultural Revolutionnote , and lastly the 1989 Tiananmen Square Massacre that the US-of-Americans are so fond of mentioning at every opportunitynote . All this censorship does a lot to explain the respect many people have for Mao Zedong despite the immense suffering he inflicted upon China's peoples, for one thing, and why there still is a Chinese Communist Party for another. There's no talk of ever publicly acknowledging this stuff, because nobody knows how the Chinese will take it and the people responsible (and their children and grandchildren, who form today's Party Leadership) have no pressing desire to find out.
- The Shooting actions and death camps of The Holocaust were an open secret in wartime Germany, since everyone knew someone (who knew someone [who knew someone]) who was involved in the process and people in general are both curious and gossipy. Interestingly most German military personnel, policemen, civil servants, and civilians later claimed that The Holocaust had occurred in such remote places and under conditions of such secrecy that they only learned about it after the war. This was untrue, but many of the people who claimed this probably thought they were telling the truth. Human memory is subject to change over time as we subconsciously change our memories to fit and justify our view of ourselves and others. An important and well-documented part of this process is forgetting things which contradict our views and remembering things which vindicate them.
- Subverting and denying this trope were the main reasons that General Eisenhower made sure that as many German civilians as possible, as well as US troops in the area, visited several Work Camps (where workers who became unfit between January and May '45 who would previously have been euthanized at the recently-liberated Extermination Camps in Poland were left to die of malnutrition) before burial operations had occurred. Eisenhower wanted there to be an overwhelming number of non-Communist eyewitnesses to the atrocities so that no-one could ever reasonably say "it never happened."