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)