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Anime & Manga
- Attack on Titan: The "Wall Cult" believes that the huge, circular walls that protect the last of humanity were a gift from God, even yelling at people who touch or get near the walls. Eren notes that even just putting cannons on top of the walls took way longer than it should have because the government had to work around the cultists. Most of the members are simply religious people, but the inner circle seems to know more about the walls than it seems...
- In Unlimited Fafnir, a dragon cult exists, which has been brainwashing Tear and causing her to believe she's really a dragon, not a human. Having horns on her head only further validates it as far as she knows. The main characters attempt to un-brainwash her, by having her live as a human. Unfortunately the cult leader, also a human, has instead chosen to live the life of a "dragon", hurting and killing people using their powers, much like the real dragons that showed up 25 years before the current events in the show.
- Alan Moore's Providence reimagines Lovecraft's Church of Starry Wisdom as a mystery cult called the Order of Stella Sapiente. Boggs and Wheatley complain about the main leaders not listening to all the suggestions of its members because the former two are despised by the more snobby figures in charge. The leaders which includes Ephraim Wade have their own plans with the Booke of the Wisdom of the Star and ensure that the knowledge is kept out of reach of the Wheatleys and others.
- Skulduggery Pleasant features so many that they might as well be the entire premise....and in fact may be. Villains in Skulduggery Pleasant books are almost invariably part of some evil cult bent on destroying the world or killing everyone in it. It's getting so it feels like that is the only possible motivation, out side of maybe revenge, which exists in this series.
- Ngaio Marsh's Death In Ectasy features a cult in the mid 1930s. The murder victim is poisoned in the special beverage she drinks during a ritual. Naturally, the investigation is hampered a bit by the secrecy of the cult members.
- The real-life cult of Mithras has featured in several historical novels, among them Rosemary Sutcliff's The Eagle of the Ninth and John M. Ford's The Dragon Waiting, which each have a protagonist who's a member. In Rudyard Kipling's Puck of Pook's Hill, it's analogous to the Freemasons, to whom Kipling belonged.
- In Elantris, the aptly-named Mysteries is an enigmatic cult with a very unpleasant (and largely deserved) reputation. Turns out that it's a corrupted knockoff of the peaceful Jesker religion, but where Jesker is dedicated to living in harmony with the Dor, the Mysteries is just about hacking into it to gain supernatural powers. King Iadon of Arelon is a follower of the Mysteries, and when he's caught in the middle of sacrificing a servant as part of a ritual, his already-shaky reign outright collapses.
- Apuleius's The Golden Ass ends with the main character restored to human form by the goddess Isis and entering her cult. He undergoes a number of initiations into deeper mysteries, each costing more money than the last.
Live Action TV
- Battlestar Galactica: Mithras apparently has an analog in the Twelve Colonies of Man, but given that they're referred to as "Mithrasaries" it's possible they're not as secretive as the followers of Mithras on Earth. Apparently, old-school religious Gemenon considers them something of a protected minority.
- Monotheism in Caprica is this by necessity: monotheism is illegal on Caprica.
- The Silence in Doctor Who is portrayed as a Mystery Religion dedicated to stopping the asking of a Question - though really it is more of a Single Precept Religion than anyting.
- In Call of Cthulhu the cults that worship the Cthulhu Mythos deities are like this. They're intensely secretive because their abhorrent practices would get them imprisoned or executed in any civilized country. By the time a new member finds out what the cult is really up to they've probably been driven insane.
- The same is said of some Chaos cults in Warhammer 40000. Genestealer "cults" are the opposite due to their hive-minded nature, but their main modus operandi is to manipulate other cults which will fit the trope as a consequence.
- The setting also has the Adeptus Mechanicus, which maintains a stranglehold on Imperial technology because many of its "mysteries" include the secrets to maintaining and operating the machinery that keeps the Imperium going. (Also, their Omnissiah may or may not be a sleeping Eldritch Abomination, and it wouldn't really help their cause if that were to get out if it's true.)
- The Dark Angels chapter of Space Marines have a Mystery Cult as the foundation of their chapter teachings: recruits are taught the history and traditions of the chapter by progressing through sequential circles of knowledge, slowly illuminating the Dark Secret and subsequent Redemption Quest at the heart of the chapter.
- Shar, one of the major deities in the Forgotten Realms is usually worshiped by secret cults instead of large public temples, being the goddess of Darkness, Secrets, and Forgetfulness. And the colors of her priests are black and purple.
- The Secret Societies in Paranoia play with this trope to various degrees, with the Illuminati being the textbook example. Members know almost nothing about the group, and typically their only contact are random visits in the middle of the night by a single masked stranger delivering inexplicable orders.
- The Systems Malfunction setting features dozens of Mystery Cults of varying size and power, all engaging in one massive Gambit Pileup.
- Mystery cults are common enough in the Nobilis universe that they're available as starting contacts on the lifepath system.
- There are a number in Rocket Age. Venus has several thugee-esque murder cults that operate completely underground and are exclusive enough that the induction can kill you. Martian faiths have several sects that fall into this as well.
- Mage: The Awakening has a number of mystery cults, often used by the Awakened to guide Sleepers to true power. The Guardians of the Veil tend to use Labyrinths, hidden conspiracies that guide the worthy to enlightenment while shunting the unworthy off into temporal power, whereas the Silver Ladder tend to use Cryptopolies, political groups and secret societies that blend mundane influence with Awakened symbolism.
- In An Epic Comic, the Society of the Free Mind's inner circle is only accessible if you become a free mind. The reason for this being is that you can't actually fully comprehend the true intentions if your mind is limited to the comic.
- Futurama: The League of Robots - a secret society of well-to-do wealthy robots (that somehow ends up having Bender as a member), that ostensibly exists to mastermind the robot dream of killing all humans, but in actuality turns out to be more like a stagnant gentleman's social club.
- In general, any cult or religious organization that structures itself in this way can be considered an esoteric body.
- The Mithraic Mysteries was a cult dating to about the first-fourth centuries. Because of their mysterious nature we know almost nothing about them, beyond that they believed their god emerged from a lump of solid stone as a fully formed adult. Other than that it's pretty vague. A popular myth rose up about hundred years ago in connection with the cult which says that Christianity was based on it. The short answer is that it was very definitely not.
- The best known example were the Eleusinian Mysteries, which is believed to have been a Demeter cult that had the story as Persephone at its center, as an explanation for the passing of seasons and possibly a cyclic nature of life. There are also records of a cult of Isis in Ancient Greece.
- The best-known modern example would be the Freemasons, a loose fraternal association of secret societies which conduct their own private rituals. One difference is that the Freemasons aren't required to keep the simple fact of their membership secret, and many members display Masonic emblems on their jewelry, houses, cars, etc. However, they do tend to be more low-key about it than some of their auxiliary bodies. One of these is the "Shriners", whose members can frequently be seen wearing fezzes with the name of their "temple" (local organization) emblazoned on it in sequins and driving miniature cars around in parades.
- There is a serious scholarly debate about whether the Villa of the Mysteries in Pompeii shows initiation into a Dionysian cult, or an allegory for marriage/rite of passage. The rest of us just look at the pretty pictures. If the art is on an initiation, the process involves being whipped by a winged woman in thigh-high boots, which was probably some sort of symbolic punishment or purification.
- Scientology ranks its members according to their level of spiritual enlightenment, starting with Clear and then progressing through various "Operating Thetan" or "OT" levels. As members progress up the ranks (which—and even the Church does not deny this—usually costs money), they are said to be capable of handling more advanced Scientology teachings. The most famous of these advanced teachings is the Xenu story that leaked onto the Internet and has been parodied in various media.