The world is at war with invaders, at least that is what the rest of the world is like. Japan seems to be frozen in time. While 12 years have passed outside very little time has passed there. Ayato Kamina, a typical teenage boy suddenly finds himself thrown in a web of mysteries. He is soon to realize that the world he knows is not what it seems. Things are vastly different than he has seen in his life. Ayato finds himself the pilot of the Rah Xephon. The organization Terra most powerful weapon, which only he can pilot. Thrust into a world chaos and separated from friends and family how will he deal with this?