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