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.

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.

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

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.