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.

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.