In a world where time stands still and your neighbor's blood runs blue, 17-year-old high school student Ayato Kamina goes about his everyday existence within Tokyo Jupiter, ignorant to the world outside him, having been indoctrinated with the knowledge that all civilization but Tokyo has been destroyed. But all changes when the mysterious civilization "MU" invades his country, pouring havoc from the skies in the shape of weird beasts known as Dolems. The events that follow will bring Ayato to the enigmatic Reika Mishima, the truth behind their existence, the discovery of what and who he is, and the mighty angelic robot RahXephon.