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 RahXeph…

RahXephon is awaken by Mishima Reika, he helps out by battleling the D-1. Ayato woke up at the hospital forgetting what has happened. His mother pretends to not know what he talked about. When the D-1…

Suddenly Ayato is surprised to see his mother and two of her Dolems attack. Ayato leaves Tokyo Jupiter, and one of the Dolems kills Ayato's mother, Mishima. Ayato, kills the Dolems and leaves Tokyo …

Ayato and Haruka now arrives in Litya City, along with RahXephon, and now Ayato and RahXephon are being researched, while Ayato Meets Quon. Meanwhile Haruko is confronted by Elvy, the only other surv…

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 Megum…

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 …

Watari and Kunugi are coming back to Nirai Kanai, with an Yamato Communcations reporter, Futagami. While coming to Terra is the Alpha Squad, who join with Elvy to take the place of her killed/wounded…

Itsuki finds a stone, while examining the Dolem that was defeated in the prior episode. Itsuki takes that stone and gives it as a gift to Sayoko, for Christmas. After, he goes to the beach and invite…

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 start…

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 birthda…

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 a…

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 sh…

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 Dole…

Despite Itsuki's report saying Quon has not yet awakened, Helena has "reliable information disputing that," namely the disc that Sayoko gave to Makoto. Itsuki is mad at Sayoko for this betrayal. Futag…

Itsuki, Helena and Isshiki grew up together as students of the Bohbem Foundation. While many of the other students exhibited special abilities, Isshiki showed little talent and was considered to be n…

Megu is going through a test to become a full-fledged member of TERRA. Ayato is still depressed because he's a Mulian and everyone was keeping it from him. He's going around biting people's heads off,…

Ayato and Quon are headed back to Tokyo Jupiter. Elvy is ordered to go out and bring them back, using the Vermillion, at any cost. Even if Ayato comes back peacefully, Iishiki plans to charge him for …

All that Ayato has known about his life proves to be a lie: his mother is not who he thought she was, his old friends are spies and Tokyo Jupiter is infested with Mu. The only person he can trust is h…

While on the run from the authorities, Ayato and Asahina grow closer as they start a life together and try to blend into the rest of society. Free of Tokyo Jupiter effects, though, Asahina soon discov…

Ayato returns to TERRA amidst many changes: Isshiki is in charge, the mysterious Mishima is now a part of TERRA, and Mamoru has arrived from Tokyo Jupiter and is willing to live in the real world.

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 kno…

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 disastrou…

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 D…

The fight with the Dolems begins. Many human lives are lost, including Cathy and John. Ayato joins with Ixtli and the RahXephon transforms.

Tensions mount as the survivors struggle to rebuild their lives among the ruins of Japan. As arguments become heated, Haruka questions her sanity as she begins to see Ayato in various places. Meanwhil…

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.