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.

After Celebrating New Years, it's back to the beach. Quon wanders off, and Ayato follows her. They come up to ruins located in the forest. Apparently Quon and Ayato go missing, and and Haruka starts a search to find them. Quon and Ayato are off somewhere, and Haruka's search was stopped due to the fact they were no where to be found. Haruka ends up back at the ruins, where Quon and Ayato reappear in front of her again.

B-story line: While Ayato and Quon are missing, Itsuki tries to pilot the RahXephon, but fails to do so.

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.

Ishiki plans to destroy the barrier around Tokyo Jupiter. Souichi is planning on tricking him somehow.

Ayato finds out from Itsuki that Haruka is in love with him, and is hurt that he didn't even know and he's been avoiding her.

Mamoru has been going through Ayato's stuff and has found out that he's close to Megu by listening to his cell phone message. He spends more time with her. He also finds Hiroko's diary, with the blue blood and the good-bye message. Later, he walks outside with Megumi. Ayato finds them. Mamoru grabs Megu around the neck and says that Ayato killed Hiroko, even though he knew she loved him. He says that Ayato will have to make a choice soon, and he will no longer be human. He punches Megu in the face.