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.

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 shocked when she walks by and sees him leaving. Helena, of the Barbem Foundation sends Doctors to investigate Quon, who is in a deep sleep. A new Dolem attacks, and both RahXephon and the Alpha Squad is sent out, but Ayato becomes distracted when he finds Quon inside RahXephon with him...

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 treason. Haruka asks to go with Elvy secretly, and she lets her. Ayato is almost to Tokyo Jupiter when Elvy catches up, and the two are about to fight when a Dolem appears to help Ayato. It distracts Elvy long enough for him to get through, then goes through too. Elvy also goes in after them. Ayato awakes in the hospital. His mom comes to get him and Quon stays there. On the way home, Ayato sees his friends and talks to them. Asahina freaks out, saying something's wrong and she's forgetting things. Mamoru tells her she's being paranoid. When Ayato gets home, he checks his blood, which is red. His mother shows him hers, which is blue. He starts to scream, and Quon wakes up.

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 his old school friend, Hiroko Asahina. Together they decide to escape the city for the real world

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. Meanwhile, Quon prepares to make her final move.