Two weeks have passed since Ayato and Reika arrived in the "real world" of Nirai-Kanai. As Ayato undergoes training to become a pilot for RahXephon, Reika continues to be tested by TERRA's scientists as they attempt to ascertain the strange bond she shares with the mythical robot.

A school friend of Ayato's, a recent refugee from Tokyo Jupiter, brings tidings and memories from home, but her motives are more than friendly. As further secrets about the MU come to the fore, Ayato resolves to see for himself the exact nature of the frightening conflict both he and Reika are now in the very middle of. Hijacking the RahXephon and re-entering Tokyo Jupiter, Ayato's encounter with his mother sheds a disconcerting new light on the very nature of his existence.

Story by Yutaka Izubuchi and BONES and Art by Takeaki Momose.