Ayato Kamina's life as a high school student is disrupted when Tokyo is invaded by advanced fighter jets. He meets Haruka Shitow, who claims to be from TERRA, a government organization trying to break through the barrier surrounding Tokyo, which was created by the Mulians to isolate and take over the city. Haruka's revelation sparks panic in Ayato, and he flees, eventually meeting Reika Mishima, who leads him to the Shrine of Xephon. There, Reika's singing awakens an unknown power in Ayato, connecting him to the being RahXephon, which emerges from an egg. As the Mulians and TERRA vie for control, Ayato's sense of identity becomes increasingly disjointed.