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. In these episodes, Ayato finds himself pursued by both his friends and his enemies. To add to his distress, Ayato discovers secret power source of the Dolems, which is far more disturbing than anything he could have imagined.