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.

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.

Itsuki, Helena and Isshiki grew up together as students of the Bohbem Foundation. While many of the other students exhibited special abilities, Isshiki showed little talent and was considered to be normal. When Isshiki finds a stone-like creature, his desire to protect it awakens something within him that he never realized he had.

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.

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

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 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.