| ShortSummary | - --04-01
- The special Plusculus edition of the [[#RahXephon video game
- Combat between the Mu and the "Normal" humans breaks out in full, with the skies swarming with Dolem. Evacuation is completed. After the previous false start, Ayato and Quon now dive into the tuning with both feet.
- Ayato is hindered in his escape by the same Dolem. The stalker, Haruka, is held safe by the RahXephon, but Reika stands on its shoulder as it is hit by an energy blast. Haruka shows Ayato the truth about the world. Ayato and Haruka wait with the RahXephon outside Tokyo Jupiter.
- Quon awakens from a coma-like sleep and escapes from TERRA with Reika. At the same time, a Dolem appears. Quon reaches for a black egg that seems very similar to the egg Ayato found inside Tokyo Jupiter.
- A Dolem that killed operator Kim Hotal's parents re-appears, but Ayato is not willing to give her the revenge she desires. Commander Kunugi and Director Watari are away dealing with the media, so Yagumo is left in charge.
- Megumi is looking forward to a promotion and confessing to Souichi. Ayato is not coping with being a Mulian. Rikudoh tells Haruka about how Maya was found and how she ran away for Tokyo. Quon tells Ayato that she is a Mulian too, and they set off for Tokyo.
- A flashback episode to when Itsuki, Helena, and Makoto were being raised at the Bähbem manor. Makoto finds a Mud Doll and decides to take it back to its mother and father.
- Ayato is transported by aircraft carrier to TERRA's base. On the carrier, Ayato meets Quon and TERRA's commander. Ayato is locked up because TERRA considers him a threat. But Quon notices a threatening timbre.
- Haruka investigates Quon, but the audience learns more about Haruka than about Quon. A Dolem appears to call Quon, but Ayato destroys it.
- Ayato, Hiroko and Mamoru are on their way to a chemistry test with a stalker on their tail. Tokyo is suddenly invaded by futuristic fighters, and giant Dolem defend the capital. In the rubble Ayato encounters Reika Mishima. Ayato is arrested, but he's freed by his stalker; Ayato runs away from her with Reika.
Ayato and Reika get on the subway and reach a special station called "The Shrine of Xephon" under Tokyo Bay. There, they discover a Dolem in storage, and further in they find a room with a blue sky, and a giant egg resting in a pool of water. The Dolems singing above affect Ayato, but Reika breaks through them with a song of her own. Suddenly the egg cracks, revealing wings inside, and Ayato says "Rah...Xephon".
- Elvy and Haruka go out in the Vermillion to intercept Ayato and Quon, but a Dolem appears and fights the Vermillion, and they are unable to stop Ayato and Quon. They all enter Tokyo Jupiter. Ayato meets Maya, Hiroko and Mamoru.
- The fighting comes to a head, with rising body counts and a rapidly diminishing list of characters left alive.
- A Dolem swallows Ayato and shows him visions of Tokyo Jupiter, his mother, and his friends. But the visions of Haruka are the scariest ones.
- Hiroko and Ayato escape from Tokyo Jupiter with the Mu, TERRA, The Bähbem Foundation, and the reporter Futagami all chasing them. Hiroko is too scared to tell Ayato about her blood turning blue. A dolem then appears and Ayato fights it. However the dolem is connected to Hiroko and once Ayato defeats the Doelm, Hiroko dies.
- It's the new year on Nirai-Kanai. The weather is still unusual, and those who can hit the beach and go for a boat trip. Quon listens to Haruka's music. Then Ayato and Quon run off together, finding a shrine on the island.
- Helena has learned more about Quon's state of awakening than what Istuki had intended, and she brings a Vermillion. Ayato and Elvy both learn why Ayato was locked up earlier. The RahXephon and Ayato give their first glimpse at being able to "re-tune", but only one person is truly aware of it.
- A reporter starts an exclusive investigation on TERRA. TERRAs Alpha Squadron is replenished with new pilots after the losses in Overlord. The squadron commander, Elvy, takes a solo risk against a Dolem.
- Nirai-Kanai is evacuated before an approaching Dolem, while one person stays behind to operate the defense systems.
- Makoto replaces Kunugi as commander, and brings with him a new staff member. Mamoru seems to have successfully escaped from Tokyo, but a new Dolem follows him.
- TERRA plans another operation against Tokyo Jupiter. Quon is again settled in at the Bähbem Foundation. Mamoru pays a visit to TERRA's deposed commander, and he discovers what has happened to Hiroko.
- Ayato's distressed feelings causes the RahXephon to petrify. Head scientist Kisaragi and second in command Yagumo come up with a plan to resolve the situation. Ayato is settled in with the uncle of Megumi and Haruka; he reminds Megumi to "not do unto others".
- Operation Downfall commences, and Ayato and Quon start entering the tuning. But Ayato is not comfortable with accepting Reika.
- The Christmas season is beach season on Nirai-Kanai, and the closest thing to snow is the decorations at Kisaragi's much anticipated Christmas party. But this year, a Christmas cheer-up for his assistant goes overboard.
- The RahXephon defeats the invaders as well as one of the Dolem. Ayato is taken home by his mother, who insists that there were no such things floating in the sky; Ayato, Reika, Hiroko and Mamoru all seem to be all right in school the next day. The stalker invites Ayato to meet again.
- TERRAs operations commander takes a rare day off, giving an opportunity for re-visiting the past. Quon and Ayato help search for harmony.
- Ayato wakes up on the modified La Grande Famille by René Magritte and enters the subway station, finding Quon. He asks her what to do, and promises to be gentle in the tuning.
Sayoko stabs Itsuki to death and Bähbem reveals that Sayoko was programmed to love Itsuki. Nevertheless, Itsuki says he has found his blue bird and dies content.
Prodded by Megumi, Haruka joins the tuning; as a consequence, Maya joins as well. Maya comes to terms with the fact that Ayato wants Haruka more than he wants a pure Mu world. Bähbem is robbed of his view of the tuning by a bullet from Takeshi.
Ayato defeats Quon and re-tunes the world to one where he was not separated from Haruka. They are married and have a daughter named Quon. Haruka gets off the phone with Megumi and Hiroko and Mamoru are invited to a class reunion. Ayato has just finished a painting of a girl in a yellow dress looking out over the sea. Haruka asks coyly who the girl in the picture is, and it is explained through a Coda that the girl that Ixtli copied her appearance from was a young Haruka.
- Ayato and Hiroko are given proof that their friends and family were not what they appeared to be. Hiroko is scared away by Mamoru and begs Ayato to escape with her.
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