Episode list

Ayato is just a normal teenager until there is an attack on Tokyo.

Ayato gains insight into Reika's enigmatic nature.

In the RahXephon, Ayato got a shock because he lost Reika and saw Maya shedding blue blood. He then operates the RahXephon to crush one Dolem, and goes outside through the barrier with the female pursuer, Haruka. She later tells him that a spherical barrier has been covering Tokyo, which called Tokyo Jupiter, and implies that the time passes more slowly in the barrier than outside.

Ayato is tested to see if he is Mulian.

Ayato is taken to his new home.

Director Watari, Commander Kunugi, and the advisor Makoto Isshiki attend a press conference, leaving Souichi in charge of it. Kim takes offense at Ayato for his thoughtless remarks, which makes him serious about the MU issue.

Elvy tries to take on a Dolem on his own.

They prepare a Christmas gift to someone special. Dr. Kisaragi finds a crystal stone on a broken Dolem that Ayato defeated, he gives it to Sayoko as a gift for the purpose of observing what happens.

Futagami investigates what happened to the island. Quon leads Ayato to a small shrine after they saw a vision of Raika. Dr. Kisaragi tries to launch the RahXephon with Sayoko and Makoto.

Kunugi's departed daughter's composition proves to have strange qualities.

The Dolem catches Ayato with the RahXephon during the battle, and takes him into a nightmare.

Quon has fallen into a strange catatonic state and is hospitalized. But then to everyone's surprise, she suddenly vanishes, and the search is on to find out just where it is that she went.

The question that seems to be on everyone's mind is just who Quon really is. Itsuki claims that she is his sister, but other things are coming to light that prove that may very well be a lie.

A shake up at the base takes place when the corporate interests use their influence to take charge of Quon. A new Terra weapon, The Vermillion, debuts and it's made known that The Foundation granted TERRA it's use.

The present becomes the past as the focus shifts to the Bahbem Foundation. Three young children live there as students, but Isshiki has found a Dolem living in the ruins beneath the mansion and wants to protect it.

Haruka asks her uncle about his daughter, Maya. Quon prepares to leave the TERRA. Ayato suffers for his identity. Megumi notices that Souichi and Kim have a close relationship.

TERRA sends Elvy to catch Ayato and Quon, as well as bring back the RahXephon. Though returning to Tokyo Jupiter may have seemed like a fantastic idea, Ayato quickly learns that much has changed.

Ayato's life is falling apart. It seems that his only salvation is with Hiroko, and together the two decide to leave the Mu infested Tokyo and return to the safety of the real world.

Megumi and Elvy make it back to the Vermillion but the RahXephon has been lost due to a magnetic storm.

Ayato returns to TERRA and finds out Isshiki has take over the command and they have a new cadet that resembles Reika.

Makoto presents the Operation Downfall, which breaks the Tokyo Jupiter's barrier. Ayato's words and actions unintentionally disturb Dr. Kisaragi and Sayoko more than ever before. Mamoru sees Hiroko's face in Megumi, but he tries to take advantage of her as his revenge to Ayato.

Issihiki receives an order to cancel operation Downfall but ignores it.

Ayato comes to terms with everything that has happened to him and by doing so regains his past.

Futagami shows up as Jumonji from Federation Division 6 and orders Lilia Litvyak and the other TERRA ships to unload the evacuees and join the Federation forces.

The remaining TERRA forces use the TDD unit on Elvy's plane to destroy much of the Mulian units.

With their godlike powers, Ayato and Quon travel through the spiritual world while adjusting the real world. He finally remembers his past with Haruka during the trip. What future will they choose?