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 is tested and found out to be normal, minus the symbol on his torso, Quon has one as well. While Ayato meets, Soyoko a co-worker and finds out he will be living with Haruko and her sister Megumi, and their uncle Rikudo. Meanwhile Itsuki finds out, that Quon is his sister. When Ayato is unpacking, he finds Buchi, which Quon packs for him. And after the dinner Rikudo gives Ayato a name plate.

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...

Ayato and Quon are headed back to Tokyo Jupiter. Elvy is ordered to go out and bring them back, using the Vermillion, at any cost. Even if Ayato comes back peacefully, Iishiki plans to charge him for treason. Haruka asks to go with Elvy secretly, and she lets her. Ayato is almost to Tokyo Jupiter when Elvy catches up, and the two are about to fight when a Dolem appears to help Ayato. It distracts Elvy long enough for him to get through, then goes through too. Elvy also goes in after them. Ayato awakes in the hospital. His mom comes to get him and Quon stays there. On the way home, Ayato sees his friends and talks to them. Asahina freaks out, saying something's wrong and she's forgetting things. Mamoru tells her she's being paranoid. When Ayato gets home, he checks his blood, which is red. His mother shows him hers, which is blue. He starts to scream, and Quon wakes up.

All that Ayato has known about his life proves to be a lie: his mother is not who he thought she was, his old friends are spies and Tokyo Jupiter is infested with Mu. The only person he can trust is his old school friend, Hiroko Asahina. Together they decide to escape the city for the real world

Ayato returns to TERRA amidst many changes: Isshiki is in charge, the mysterious Mishima is now a part of TERRA, and Mamoru has arrived from Tokyo Jupiter and is willing to live in the real world.

The fight with the Dolems begins. Many human lives are lost, including Cathy and John. Ayato joins with Ixtli and the RahXephon transforms.

Tensions mount as the survivors struggle to rebuild their lives among the ruins of Japan. As arguments become heated, Haruka questions her sanity as she begins to see Ayato in various places. Meanwhile, Quon prepares to make her final move.

The RahXephon has transformed into its final state and the battle between the Xephons has begun. The outcome will not only determine the fate of Ayato and his loved ones but also the world.