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

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.

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.

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.