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 dolem is beating RahXephon, and Ayato is writhing on the floor of the cockpit, and is in a dream state where, Toyko is much different, there are flashes of a Murian, Mamoru, Hiroko, Haruka Mishima and his mother.

Ishiki plans to destroy the barrier around Tokyo Jupiter. Souichi is planning on tricking him somehow.

Ayato finds out from Itsuki that Haruka is in love with him, and is hurt that he didn't even know and he's been avoiding her.

Mamoru has been going through Ayato's stuff and has found out that he's close to Megu by listening to his cell phone message. He spends more time with her. He also finds Hiroko's diary, with the blue blood and the good-bye message. Later, he walks outside with Megumi. Ayato finds them. Mamoru grabs Megu around the neck and says that Ayato killed Hiroko, even though he knew she loved him. He says that Ayato will have to make a choice soon, and he will no longer be human. He punches Megu in the face.

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.