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

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.

Haruka visits the Great War Memorial Hall, where an unidentified source informs her documents showing Quon was in Sendai are probably fakes, and at dinner, we get hints that Ayato likes Haruka. A Dolem appears, but since it is too high up to effectively attack, and hasn't made any offensive moves, and TERRA lets it be. Sayoko spends most of this episode sneaking around, trying to get information out of people, with varying success.

Megu is going through a test to become a full-fledged member of TERRA. Ayato is still depressed because he's a Mulian and everyone was keeping it from him. He's going around biting people's heads off, accusing them of laughing about him behind his back. Haruka is worried about telling Ayato some secret. The two of them talk. Haruka says that it doesn't matter that Ayato is a Mulian, but he doesn't listen. Sayoko breaks it off with Iishiki, saying that he was using her, but she was also using him. She gives him a dress as a token, because she no longer has anyone to wear it for. And Quon is about to be moved to her new home. Megu passes her test and she is going to meet someone to tell him about her feelings for him. But when she goes to meet him, she finds that Souichi is already in a relationship with Kim. She's upset at first, but Kim starts to cry, so Megu forgives her. Quon asks Ayato to take her to Tokyo and he agrees, flying off in the RahXephon.

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.

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

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.