The series subverts its own core mythology through several major plot revelations:
- The Reality of the Blue Moon Vampire (Luna): Contrary to orthodox vampire myth painting the Blue Moon vampire as a vengeful demon, Luna was a protective, lonely figure who rescued Vanitas (Number 69) and Mikhail (Number 71) from Dr. Moreau's torturous laboratory.
- The Death of Luna: Vanitas did not kill Luna out of hatred; Luna was infected by a malnomen/curse that began corrupting them, forcing Vanitas to use the Book of Vanitas to mercy-kill the person he loved most. Vanitas's crusade to heal vampires is driven by unresolved guilt and his inability to save Luna.
- Mikhail's Return: Mikhail, Vanitas's surrogate brother from Moreau's lab who possesses a second Book of Vanitas, returns driven by an obsessive desire to resurrect Luna. Mikhail holds Dominique hostage to force Noé to drink Vanitas's blood, triggering the climactic rooftop duel between Vanitas and Noé.
- The True Nature of Naenia / Charlatan: Naenia is revealed to be the corrupted, distorted shadow form of the vampire Queen Faustina, acting under the subtle machinations of Noé's Teacher, the Shapeless One (Sensei), who is orchestrating events behind the scenes to manipulate the World Formula.