Set in the year 2015, just after Earth's civilizations have been all but wiped out, RAHXEPHON finds a high school student named Ayato Kamina struggling to escape the rubble after an attack on his city left him trapped. Finally freeing himself from the debris, Ayato meets a girl named Reika Mishima who takes him to a secret sanctuary that houses the war's civilian survivors. There, a humanoid mechanical weapon emerges from a black egg when he arrives bearing the same marking as one Ayato has on his body. It becomes apparent that Ayato is the only one who can pilot the weapon, and he soon realizes that he might be the only person able to defend the world from more destruction.