In the aftermath of a catastrophic event that isolated Tokyo from the outside world, Ayato Kamina's life is forever changed when invaders suddenly descend upon the city. Haruka Shitow, a member of TERRA, appears and reveals the truth about the world, setting Ayato on a journey that involves piloting the powerful mech, the RahXephon, and discovering the existence of a self-enclosed dimension where time passes differently from the outside world. As Ayato uncovers the secrets of his own existence, he learns that his mother, like many others, possesses a mysterious trait - blue blood - and that his entire life has been a façade.