Empire with a Dark Secret

Hey, guess what? Your entire civilization lives on a lie. It might be a secular version of a Path of Inspiration, or maybe no one in the world has ever realized that the Applied Phlebotinum powering your homes and healing your sick is actually Powered by a Forsaken Child - but in any case, Utopia Justifies the Means, right?

The publication of this verboten knowledge by an Intrepid Reporter might spell doom for all civilized society, incite universal rebellion, or simply make you Go Mad from the Revelation.

So play nice and don't delve any further, capiche?

Anime and Manga

 * 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 Soukou no Strain, 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 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 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 they've 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.
 * Another dark secret might be what the Evangelions actually are.

Fan Works

 * There's more than one Axis Powers Hetalia fic that posits the existence of the Nations themselves as this trope. Depending on how dark the story is, it usually results in mass chaos and What Measure Is a Non-Human? scenarios.

Film
""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 Alliance from Serenity had buried the fact that some time ago, they
 * 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.
 * It's not really a dark secret though is it?
 * Only in that it means Earth is repeatedly in cosmic peril and almost everyone on Earth remains in blissful ignorance.

Literature

 * The Wheel of Time's 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.
 * 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, about one in three are taken by "the bleakness": putting down their weapons and just walking off into the desert.
 * 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 . Needless to say, things get ugly.
 * Scott Westerfield likes this Trope. The society in Uglies relies on the government performing operations on everyone that cripple their ability to think independently, and it's enforced by Super Soldiers.
 * 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
 * Borogravia in Monstrous Regiment. Turns out
 * Germany in the book Fatherland.
 * 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 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
 * 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.
 * 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,
 * 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 cause a lot more damage than she knew.
 * 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.

Live-Action TV

 * In the Doctor Who episode "The Beast Below",
 * There's also the fact that . Or simply someone who doesn't do his homework. Luckily,.

Music

 * Hades in the folk opera Hadestown tells his Underworld subjects that he's keeping them safe from an enemy that doesn't actually exist.

Tabletop Games

 * 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.
 * To be fair, he was actually more of a Nay Theist who acknowledged the existenc of the Chaos Gods, but tried to suppress all religion in the hopes of starving them to death. To be even more fair this plan was doomed from the start, because the gods of the Warp feed on emotions in general, and not just the faith of their followers, so the fact that the Imperium is revering him as a God-Emperor who fights the forces of Chaos in the Warp and keeps the universe safe is actually a pretty good plan, because enough people believing it helps make it true, and if the Imperium at large found out and lost their faith the likely result is that he would die and Chaos really would win. That the secret is still pretty sinister is just another sign of of how much a Crapsack World the 40K verse is.
 * 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.
 * 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.

Video Games

 * 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.
 * In Chrono Trigger, the highly magical floating continent of Zeal has a dark secret ---all of its magic comes from
 * In Grandia II, Roan finds out that his people are and decides they.
 * 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, X.
 * The Jade Empire. Rain only falls because . Oh, and Emperor Sun Hai   Oh, and.
 * In Mass Effect 3, it is revealed that the Asari, who didn't become galactic top dog by being wisest and smartest,
 * 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 has been secretly been creating a Zerg hybrid.

Real Life

 * This can also be a Truth in Television, for instance:
 * The corruption and violence of the French colonial empire was a big taboo in French society until its collapse and it kept existing until today. Many French today still do not know that one of the worst famines in history happened in Algeria after France conquered it.
 * 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 imperialism. The people they conquered are not happy with that portrayal.
 * In fact, just about any country with a history of imperialism that wants to promote national pride in the present day is apt to suffer from this trope to some extent. Imperialism is an ugly business and the best way to deal with that ugliness, in the minds of some 'patriots', is to sweep it under the carpet and focus on the 'good' parts. Let's not put any specific examples just because you as troper think it might count.
 * In the Soviet Union, the existence of the Molotov-Ribbentrop Pact with Nazi Germany was vigorously denied by the Communist authorities until 1989.
 * Same with the 1940 massacre of Polish officers in Katyn, which the Soviets blamed on Those Wacky Nazis between its discovery in 1943 and 1990.
 * Sometimes, the Empire's Dark Secret isn't on the Empire's own soil and its terrible crimes aren't done by Empire's own hands. USA has been supporting dictators in Latin America and Middle East (and probably other places, too) to secure USA's own interests—even as the government of USA keep on blaring at the average Joe American about how USA is the champion of human rights in the world. For example, Saddam Hussein was initially a check against Iran and Hosni Mubarak was a check against the Muslim Brotherhood.
 * That's not really a dark secret in here in the United States, though. We know that our government has aided tyrants in the past (and probably in the present) and we are NOT HAPPY ABOUT IT.