Earth Federation officer Makoto Isshiki watches as the Lilia Litvyak docks at Nirai Kanai Island. On board Ayato gets a blood test and Haruka is relieved to see his blood is red. Jin Kunugi, commander of TERRA, enters and asks about the cat. Ayato says he won’t help them and Jin says Ayato should set his watch to the correct time. Later, Jin is briefed by an Earth Federation captain that they are taking the RahXephon and have no need of Ayato. Haruka looks for Buchi the cat, and Ayato asks what Jin meant about the time. Haruka shows Ayato her watch, which shows the 12 year time difference. Haruka sends Ayato ahead while she goes to talk to her friend, Elvy Hadhiyat. Elvy asks if Haruka thinks the lives of her men were worth one kid. Ayato finds himself at the ship barber shop where he runs into Quon Kisaragi. She asks him to help her get her life module on and then drags him off, calling him Ollin. They go outside and see the RahXephon being transferred. Ayato wonders what they’re doing and Makoto appears, saying they can do what ever they want with their spoils of war. Ayato questions Jin about it and Jin asks if Ayato expects some sort of ownership of the RahXephon. Ayato asks what’s going to happen to him and Jin says he should become aware of his current situation. Meanwhile, the dolem Grave makes its way through the ocean.
In Ayato’s room, Haruka tries to cheer him up, but he says that outsiders have an air of superiority because they think it’s their job to educate people like him. Jin and his vice commander, Souichi Yagumo, see that Ayato’s blood has the Mu phase. Souichi wonders if Ayato is a mulian and Jin says they should treat him like one. Haruka is paged and leaves, but the door is sealed off when she leaves. She confronts Jin, begging him to let Ayato go. Quon enters and implies that a dolem is approaching. TERRA sorties its forces to intercept, but Grave easily breaks through. Grave disappears from radar and comes up from below the Lilia Litvyak, spreading its tentacles throughout the ship. Ayato bangs on the door, calling for Haruka to let him out. He realizes that she lied to him and curses. On the Earth Federation ship, the RahXephon activates and goes to the Lilia Litvyak. Quon sees a vision of Ayato reaching out to Reika and Ayato disappears into the RahXephon. RahXephon punches into Grave and pulls it into the air. It punches it again and tears Grave in two. Afterwards, the Federation captain tells Jin that TERRA can’t take the RahXephon, to which Jin replies he should take it up with the RahXephon itself. The RahXephon lands in a shrine for it as scientist Itsuki Kisaragi welcomes Ayato back.
This episode introduces much of the supporting cast, most importantly the enigmatic and therefore instant fan favorite Quon. She’s rather spacy, but is actually quite aware of what’s going on. She’ll have a big role to play in the future. We also see the human’s ability to fight off the Mu…. Which is nonexistent. They can’t so much as damage the dolem until the RahXephon shows up. Sure, it’s one of the biggest clichés out there, but it actually is rather realistic. Now Ayato is with TERRA and we’ll see how he adjusts to it.