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.

Itsuki finds a stone, while examining the Dolem that was defeated in the prior episode. Itsuki takes that stone and gives it as a gift to Sayoko, for Christmas. After, he goes to the beach and invites Ayato, Megu, and Haruka and the others to a Christmas Eve Party. And it begins to snow. While Megu and Kim are shopping Megu talks about Haruka, while Haruka gives Ayato gloves. And a Dolem appears to freeze everything. And RahXephon and Ayato must defeat it, but there's a problem, Sayoko is a part of it. And it's up to Ayato to save christmas for Nirai Kanai. When it looks in doubt, Ayato thinks of Haruka and the gloves he gave her, and saves the day.

B-Storyline: Quon stays in bed under her blanket, because she hates the snow.

Kunugi takes the day off. Quon visits him and plays some music for him, but its incomplete. She goes a little crazy because the song doesn't have an end. Meanwhile, Kunugi goes on a ship for a birthday date, talking to his former wife. She says that he didn't spend enough time with his daughter, using work as an excuse. She gives him the last part of the music. His daughter wrote the music for him. It's her birthday, but she's dead. He visits her grave. Quon finishes the song.

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...

Despite Itsuki's report saying Quon has not yet awakened, Helena has "reliable information disputing that," namely the disc that Sayoko gave to Makoto. Itsuki is mad at Sayoko for this betrayal. Futagami reveals an odd family secret.

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.

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.

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 aerial cities continue to multiply. Kunugi decides to evacuate everyone from the island and stay by himself to try to stop the D1 headed their way. TERRA leaves with everyone else. The D1 is the Dolem of Kuki, Kunugi's former superior officer that gave him the order to kill his own daughter. It reaches the island of Narai Kanai and starts destroying cities. Kunugi sends some missiles and remote control fighter jets, but they do no good. The D1 attacks the building he's in while Kuki taunts him. Kunugi is injured, and Kuki says it's over. But Kunugi tells him that the entertainment has yet to begin, and activates the barrier creating thing. The barrier destroys everything in it's path, including the cities, Kunugi, Kuki, and the D1. Ayato makes a choice to join with Ixtli in order to protect Haruka.

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.