RahXephon follows Ayato Kamina, an ordinary high school student whose life changes when Tokyo is attacked by futuristic fighter jets and he is drawn into a hidden war. In the aftermath, he meets Haruka Shitow, a member of the government organization TERRA, who explains that the city has been sealed inside a time bubble known as Tokyo Jupiter by the Mulians, humanoids from another dimension who are trying to isolate and take over Tokyo. As TERRA fights to break through the barrier and reclaim the city, Ayato is pulled toward a conflict he does not understand.
His search for answers leads him to his classmate Reika Mishima, who guides him to the Shrine of Xephon, where a large egg lies dormant. When she begins to sing, an unknown power awakens within Ayato and connects him to RahXephon, a mysterious being that emerges from the egg. Haruka soon finds him again and urges him to join her fight against the Mulians, but the deeper Ayato goes, the harder it becomes to trust his own memories.
Caught between TERRA and the Mulians, Ayato must confront the truth behind Tokyo Jupiter and the possibility that his own identity is tied to the fate of the city.