In a world where time passes at a crawl and the blood of your neighbor runs blue, 17 year old high school student Ayato Kamina goes about his daily life within Tokyo Jupiter oblivious to the world around him, having been educated with the fact that the all civilization but Tokyo has been destroyed. But all that changes when the mysterious civilization "MU" invades his home, raining destruction down from the sky in the form of strange monsters called Dolems. The events that occur next will lead Ayato to the mysterious woman named Reika Mishima, to the truth of their existence, the discovery of what and who he is, and to the powerful angelic robot RahXephon.
Ayato has returned to see Haruka...for the last time. He has become a God and now must battle Quon, who has also obtained the form of a God, in one last battle. The winner will create the world of their choosing. As Haruka and Megumi watch the battle begin from afar, Haruka feels lost. Megumi helps her sister by telling Haruka that she always wanted to be as strong as her.