When Tokyo is attacked by futuristic jets, Ayato Kamina's mundane high school life takes a sharp turn. He meets Haruka Shitow from a government group named TERRA, who discloses the existence of 'Tokyo Jupiter,' a time bubble controlled by humanoid aliens called Mulians. TERRA aims to penetrate this barrier. Overwhelmed, Ayato flees but encounters Reika Mishima, leading him to 'The Shrine of Xephon' where he unlocks a mysterious power within him, connecting him to RahXephon. As Ayato grapples with his newfound abilities, Haruka persuades him to join the fight against the Mulians, plunging him into a world of blurred memories and self-discovery.