Ayato Kamina is separated from his beloved Haruka Mishima after an event that was believed to have killed everyone outside Tokyo. Three years later, the city is suddenly invaded, and Ayato encounters Haruka Shitow, an agent of TERRA. She promises to reveal the truth about the world. This meeting sets in motion a series of extraordinary events: Ayato pilots the giant mecha RahXephon, discovers that many people, including his own mother, carry the so‑called “blue blood,” and learns that he has been living in a self‑encased dimension where time passes more slowly than in the outside world.