The Seven Ciphers of the Book of Rapture are seven phenomena deep within Xanadu. They are riddles guarding eldritch events from being unleashed on the Earth, and each riddle is guarded by a giant creature. The last three were fought by the protagonists of OH GOD THE RAPTURE IS BURNING in the second act, with the first four being revived to be fought by the protagonists in Act IV.
- Partita: The Epic Structure (Non Omnis Moriar), spawned the first Rake, revived and fought in Act IV. Partita is a giant flying serpentine monster with wings made of stained glass, a peacock's tail, and bug-like antennae on front. It flies around Xanadian locations, wreaking havoc as Shadowclones spawn on its back to attack anyone who attempts to board the Cipher. Its battle is modeled after Phalanx, the thirteenth Colossus from the video game Shadow of the Colossus.
- The Virion Complex (Aut Viam Inveniam Aut Faciam), spawned the second Rake, revived and fought in Act IV. The Complex is a labyrinthine wax hive filled with worms with spider legs. At the center of the Complex is a beating heart. Its battle is modeled after horror games.
- Telos Absent (Exitus Acta Probat), spawned the third Rake, revived and fought in Act IV. Telos Absent is a robot that must be defeated by conventional video game methods of firing repeatedly at it as it chases the protagonists until it eventually dies. Its battle is modeled after shoot-em-up games.
- The Middle Fights (Dulce Bellum Inexpertis), spawned the fourth Rake, revived and fought in Act IV. The Middle Fights are a miniboss rush filled with spidercats, Big Ones, Bipedagators, Crying Men, giant spiders, Carbras, and even another manifestation of Nyarlathotep.
- The God Machine (Deus Ex Machina), sparked the attention of The Ecclesiarchway and The Musicians. Lying dormant inside a massive cathedral, the God Machine is a cross-shaped hairy behemoth which relies on laser-based attacks. Its battle is modeled after the Temple Guardians from Metroid Prime 2.
- The Grand Gtheru (Sine Labore Nihil), greatly increased the amount and sizes of rabbit holes. The Grand Gtheru is a cross between a Guitar Hero controller and Cthulhu that must be fought in an auditorium at the top of a strangely-built tower.
- The Realm King (Morituri Te Salutamus), marked the duels of the Knights of Xanadu. The Realm King is a royal blue figure perched on a throne who rarely attacks directly, instead sitting still and allowing the protagonists to attack him all they want. His battle is modeled after unintentionally easy video game final bosses.