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)

Ayato and Haruka now arrives in Litya City, along with RahXephon, and now Ayato and RahXephon are being researched, while Ayato Meets Quon. Meanwhile Haruko is confronted by Elvy, the only other survivor from the Battle on Tokyo Jupiter. During the test Ayato is found our to be a Murian and is locked up for it by order of King Kunugi. And then Litya gets attacked by a Dolem. And Ayato must save Terra from the Dolem. After eliminating the Dolem, Ayato hands over the Rahxephon to Terra where it can be taken care of by Dr. Itsuki

Watari and Kunugi are coming back to Nirai Kanai, with an Yamato Communcations reporter, Futagami. While coming to Terra is the Alpha Squad, who join with Elvy to take the place of her killed/wounded colleagues. Meanwhile, Futagami goes to Rikudo's place, to find information for Ayato. And when Alpha Squad and RahXephon attack a giant Dolem, it releases smaller dolems. And Ayato must defeat it and does.

Itsuki, Helena and Isshiki grew up together as students of the Bohbem Foundation. While many of the other students exhibited special abilities, Isshiki showed little talent and was considered to be normal. When Isshiki finds a stone-like creature, his desire to protect it awakens something within him that he never realized he had.

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.

Eager to prove himself, Ishiki fires Haruka over a trivial matter and takes control of the attack on Tokyo Jupiter. Against orders, he moves the attack up one hour. The attack commences with disastrous results.

Meanwhile, Ayato is busy finishing up his painting when he receives a call from Kunugi to pick up Mamoru's cat. While there, he learns how Haruka saved him from the concentration camps. Returning home, he finishes his painting. He is about to show Haruka when Mishima appears and reveals her true purpose for her existence and Ayato's destiny with the RahXephon.