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.

A photographer heads out to a mysterious archeological site, but is promptly shot to death by the very woman who brought him there. At Nirai Kanai, Sayoko and Mokoto are getting together. Haruka is shocked when she walks by and sees him leaving. Helena, of the Barbem Foundation sends Doctors to investigate Quon, who is in a deep sleep. A new Dolem attacks, and both RahXephon and the Alpha Squad is sent out, but Ayato becomes distracted when he finds Quon inside RahXephon with him...

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.

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.