No matter how alluring or intriguing a conspiracy theory may sound, it's almost always a work of fiction. This is the case in reality and anime, but sometimes there really is an evil group controlling the world through minority rule.
In some cases, this conspiracy is the result of just one evil mastermind. In others, it's a group that controls society for nefarious reasons. Either way, these conspiracies' existence came as a horrifying shock to both characters and audiences.
WARNING: Spoilers ahead.
10 Monster — The Monster Was Alive & Still Loose In The World
The eponymous "monster" that the seinen classic Monster referred to was none other than Johan Liebert, but that's only the simplest way to describe a man who's practically evil made flesh. Besides using countless aliases and disguises, Johan was considered to be the literal devil, the antichrist, and many other things by victims he drove to madness.
Because of this, "The Monster" became more of a feared urban legend than a wanted serial killer. The only person who knew The Monster's true identity was Kenzo Tenma, the doctor who saved a young Johan a long time ago. Worse, Kenzo knew why Johan inflicted suffering on others: it was his twisted way of thanking him for saving his life.
9 Eden Of The East — Mr. Outside Forced The Selecao To Save Japan
In Eden Of The East, Japan was stagnating and a terrorist almost threw the country into anarchy during the Careless Monday missile strike that (miraculously) left no casualties. These two seemingly unconnected scenarios were part of a masterplan orchestrated by the mysterious extremist Mr. Outside, who wanted to save Japan no matter what.
None of these were even hinted at when Akira Takizawa showed up at the White House lawn naked with a gun and phone in hand. At most, Saki Morimi and everyone else thought he was just crazy. The truth was that he was actually Mr. Outside's ninth chosen Selecao, who were tasked with saving Japan using any means necessary under the vague threat of being "eliminated."
8 Hellsing Ultimate — Millennium Were The Vampiric Remnants Of Nazi Germany
When Hellsing Ultimate began, there was a strange uptick of grisly murders across London perpetrated by vampiric Ghouls. The solitary clue that the Hellsing Organization and Vatican Section XIII was a shady organization called "Millennium," but they never expected it to be comprised of undead Nazis right out of World War II.
Millennium ordered these attacks to distract the world and lay the foundations for their assault on London, since their goal was to die in the bloodiest war they could wage. They've been setting the stage in the decades since the war's end, and they got their funding, resources, and protection from rich ex-Nazis hiding in Brazil and even the Vatican.
7 A Certain Magical Index — Academy City Wasn't Founded With Education In Mind
Academy City may be home to the best scientific minds and the most powerful espers in Japan, but it wasn't founded out of a passion for education. The truth is that Academy City was a giant laboratory and petri dish where amoral scientists conducted experiments on the student body either subtly or out in the open.
Students usually joked about this or suspected it, but it was horrifyingly real as seen in the spin-off A Certain Scientific Railgun's dark Sisters Arc. Even this was just the beginning. Whether they realized or not, the scientists were only following Aleister Crowley's ideology, as he founded the city to find a way to supplant espers with science and technology.
6 Speed Grapher — The Roppongi Club Was More Than A Fetishist's Den
When jaded photojournalist Tatsumi Saiga was assigned to sneak into the Roppongi Club, the worst he expected to see was Japan's elite indulging in their sexual fantasies. While Tatsumi and just about everyone in Speed Grapher knew that the ruling class was depraved and immoral, they didn't expect their perversions to be so literal.
The Roppongi Club wasn't just an opulent brothel, but something akin to a cult that bestowed superpowers to its members based on their addictions and fetishes. The club is also connected to the Tennozu Group, a business conglomerate that practically controls all of Japanese society by furthering the divide between the rich and lower classes.
5 Fullmetal Alchemist — Amestris' Elite Conspired With Dante & Father Ever Since The Country's Birth
Fullmetal Alchemist and its reboot Fullmetal Alchemist: Brotherhood have a lot of differences between them, but one constant was Amestris' ruling class and government conspiring with nigh-immortal evils. These were Dante (left) and Father (right), respectively, and they were the heads of sprawling conspiracies that date back to Amestris' founding.
Both ruled the government from the shadows, ordering them to commit atrocities and corrupt practices for their long-term goals. Where Dante wanted to maintain her immortality, Father plotted to usurp god themselves. Either way, the conspiracy theories claiming that Amestris' elite were evil for reasons beyond mere corruption were both true.
4 Attack On Titan — The Royal Government Were Pawns In A Worldwide Conspiracy
The Royal Government's corruption and lack of ethics was an open secret in Paradis, but what many never realized was that there was actually a reason to their madness. Some people (most notably Erwin Smith's father) theorized that there was actually a world beyond the walls, but they were violently silenced by the government.
This was done not just because the ruling class wanted to maintain its power, but to bury one of Paradis' darkest secrets. The truth was that Paradis was really ruled by the Reiss Family, and the monarchy was just its public faces. Additionally, Paradis had to be isolated at all costs, lest they risk the world's hatred towards its Eldian populace.
3 Psycho-Pass — The Sibyl System Should Never Have Been Trusted
As far as Japanese society was concerned, the Sibyl System was a great convenience – even if it did come at the cost of their privacy and agency. This is why when Shogo Makishima and his followers mounted a rebellion against Sibyl, they were viewed as terrorists with a broad grudge against "society" rather than anyone in general.
For Shogo, destroying Sibyl was the only way to achieve true freedom – even if doing so could cause Japan to collapse. The thing is, nobody expected Sibyl to be more human than anticipated. Specifically, Sibyl was a hive mind of sociopaths' disembodied brains, and they controlled the fates of millions of people by coldly calculating who was useful to society and otherwise.
2 Steins;Gate — There Really Was A War For Time Travel & The World's Future
As part of his mad scientist gimmick, Rintaro loudly proclaimed that The Organization was trying to assassinate him. Who or what exactly The Organization was and why they wanted to kill him was irrelevant; it was just part of a fun act. In a horrifying turn of events, there really was a clandestine group trying to kill Rintaro, namely SERN.
SERN was the European Society of Nuclear Research, and they wanted to steal Rintaro's time travel innovations to rule the world. Opposing them were rebels including a time-travelling Suzuha Amane, who fought to avert SERN's dystopia. Rintaro found himself in the middle of this civil war when he accidentally turned his microwave oven into a time machine.
1 Neon Genesis Evangelion — SEELE Was A Centuries Old Doomsday Cult
SEELE knowing how and when to exactly fight the Angels never sat right with anybody, whether it was the UN, Japan's government, or SEELE's armed division NERV. Everybody had their suspicions about what SEELE really wanted and how they were connected to the fated Third Impact, but nobody expected them to be actively ending the world.
By making true the apocalypse as written in the Dead Sea Scrolls, SEELE hoped to "save" mankind from its worst tendencies by forcibly ending human individuality through the Human Instrumentality Project. SEELE has been plotting this for centuries and by the anime's present, they were just a few steps from achieving Armageddon.