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)

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.

A photographer heads out to a mysterious archeological site, but is promptly shot to death by the very woman who brought him there. At Nirai Kanai, Sayoko and Mokoto are getting together. Haruka is shocked when she walks by and sees him leaving. Helena, of the Barbem Foundation sends Doctors to investigate Quon, who is in a deep sleep. A new Dolem attacks, and both RahXephon and the Alpha Squad is sent out, but Ayato becomes distracted when he finds Quon inside RahXephon with him...

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.