In the year 2012, Tokyo is suddenly attacked by a mysterious organization called "MU". At that time Ayato Kamina is just a regular high school student. His father passed away when he was young, and his mother works for government. Ayato meets a mysterious woman named Reika Mishima and discovers the existence of the angel-winged giant robot, Rexephon. Apparently Rahxephon synchronized with Ayato. So could he the key to save Japan?