The city of Tokyo has been overthrown, taken over by the Mu, invaders who have devastated the rest of the planet. Within the domed walls of the city, time flows on a different path, and none of the citizens even know they've been invaded and conquered. After a subway accident high school student Ayato Kamina stumbles into a gigantic egg from which the mecha RahXephon hatches and bonds with Kamina propelling him into the outer world. Outside Tokyo, the remnants of the human race have fought a desperate 15 year war against the Mu, knowing only that the key to victory lies within the occupied city. A mystery unfolds as Ayato confronts a world he has never known, and begins to learn the horrifying secrets of RahXephon, a humanoid super weapon which apparently only he can control.