RahXephon is awaken by Mishima Reika, he helps out by battleling the D-1. Ayato woke up at the hospital forgetting what has happened. His mother pretends to not know what he talked about. When the D-1 was recovering in the labotory, Ayato met Haruka to know the truth, Haruka wanted to go back to the real world, but Mishima summoned RahXephon. RahXephon destroyed the D-1, discover that her mother has blue blood and went to the real world by passing the barrier.

(Sypnosis came from www.animeinfo.com)

While on the run from the authorities, Ayato and Asahina grow closer as they start a life together and try to blend into the rest of society. Free of Tokyo Jupiter effects, though, Asahina soon discovers something about herself that frightens her. Fearing that Ayato would leave her if he knew her secret, she decides to keep the news to herself.