On Tokyo Jupiter, a 17yr old boy, name Ayato, is living a normal life until, Tokyo Jupiter is attacked. When Ayato is saved by Haruka, Ayato cracks an egg which released a structure, known as RahXephon, to fight against Mu.

14 Years ago a Dolem apppeared. Now the same dolem is back, and killing people in Australia. Kim Hotal get's an unauthorized sound bite due to the fact that Dolems use these sounds for their attack patterns! Now, Terra must wait for the Dolem to appear, and Ayato must be ready to attack. And when it does, Can Ayato win? Ayato comes out the winner!

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.

A dolem is beating RahXephon, and Ayato is writhing on the floor of the cockpit, and is in a dream state where, Toyko is much different, there are flashes of a Murian, Mamoru, Hiroko, Haruka Mishima and his mother.

Eager to prove himself, Ishiki fires Haruka over a trivial matter and takes control of the attack on Tokyo Jupiter. Against orders, he moves the attack up one hour. The attack commences with disastrous results.

Meanwhile, Ayato is busy finishing up his painting when he receives a call from Kunugi to pick up Mamoru's cat. While there, he learns how Haruka saved him from the concentration camps. Returning home, he finishes his painting. He is about to show Haruka when Mishima appears and reveals her true purpose for her existence and Ayato's destiny with the RahXephon.