After a catastrophic event seemingly wipes out life beyond Tokyo, Ayato Kamina reunites with his lost love, Haruka Mishima, amidst a sudden invasion by unknown forces. Recruited by TERRA agent Haruka Shitow, Ayato delves into the enigmatic truth of his reality. As he pilots the RahXephon, a colossal mecha, he unravels the mystery of individuals with blue blood, including his mother, and uncovers the unsettling time differential in his isolated dimension.