While cults aren't particularly common in anime, their inclusion makes for some seriously twisted storylines. They can produce some of the creepiest villains imaginable, even though some of them turn good when the brainwashing wears off. They can also provide some truly sympathetic backstories for all kinds of characters.
While some use the word to refer to any new religion, a cult needs to have a few specific features in order to qualify. According to psychiatrist Robert Jay Lifton, a true cult requires a charismatic leader, an initiation ritual that brainwashes inductees, and coercive motives. Anime cults manage to achieve all of these prerequisites, and because they exist in a fantastical, animated world, their sick goals often put the most terrifying real-life cult stories to shame.
The Cult of the Sacred Eye is one of the most disturbing details of Future Diary, and that's saying something, considering that the main character is a girl who locks her parents in a cage to stop them from abusing her.
The cult believes that a young blind girl named Tsubaki is clairvoyant, and they worship her for it. If that was all they did, things wouldn't be so bad, but the cult quickly goes downhill when a high ranking officer named Funatsu kills Tsubaki's parents and takes over the group. From there, Funatsu decrees that followers can cleanse themselves of sin by raping Tsubaki. The traumatic experience pushes Tsubaki to use the cult to attempt to destroy the world, as she blames it for her suffering.
Walls play a crucial role in Attack on Titan; they're the only things that stop man-eating monsters from devouring people, so they symbolize safety and security. Unfortunately, some people take their wall love a little bit too far, which leads to the Church of the Walls.
The Church of the Walls is a powerful religious organization that consider walls to be gifts from God. They believe that the walls that protect them should not be altered in any way, and object to the idea of adding defensive weapons that might increase their chances of survival. Their reasoning is not entirely religious, as some of the upper members of the cult know that the walls contain Titans, and they're trying to keep this information under wraps.
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The Church of Leto forms up around the wicked Father Cornello in FMA: Brotherhood. Cornello is a false prophet who sets up shop in the rural desert town of Reole, and who claims to be a "messenger of God." As soon as the Elric brothers arrive on the scene, it becomes clear that Cornello is using alchemy to convince the public of his divine right, so that he can amass an army of followers to take over the world.
When Ed and Al try to convince their contact Rose (who is a member of the cult) that her religion's leader is a fraud, Cornello sways her by saying that he can use his powers to bring back her dead boyfriend. After several confrontations, Ed secretly broadcasts Cornello's admission of guilt on the town's PA system, which causes his followers to lose faith. After this happens, Cornello seeks out the homunculi, only to be killed by Lust and devoured by Gluttony.
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One of the only things that Hidan of Naruto ever talks about is Jashinism, the cult religion that he belongs to. Followers of Jashin are tasked with creating as much destruction and pain as possible, and they prove their devotion via blood sacrifices. Due to the cult's sinister experiments, Hidan is functionally immortal, which makes killing others in service of Jashin super easy.