Plot:
The unusual relationship between Ayato Kamina and Haruka Shitow is one of the most important plot lines of the series. Although Haruka appears to be a stranger to Ayato at first, the series reveals that Haruka and Ayato know each other from before the beginning of the story.
Ayato, a boy conceived with the help of the Bähbem Foundation, was living in Tokyo with his adoptive mother, Maya Kamina. Ayato met Haruka on a trip outside Tokyo, and they continued seeing each other when they returned to school in Tokyo. At this time, Haruka’s family name was Mishima.
However, during what later became known as the Tokyo Jupiter incident, Haruka Mishima and her pregnant mother were away on a holiday trip while Ayato was caught inside. Years later Haruka’s mother re-married and their family name became Shitow. Meanwhile, Maya modified Ayato’s memories to make him forget Haruka. The series makes clear that the entire population of Tokyo Jupiter is subject to the same kind of mental control. Still, visions of Haruka continue to haunt Ayato, as manifested in his art. Ixtli, RahXephon’s soul, also adopts Haruka’s appearance and family name (Mishima) but takes a different given name, Reika.
The story begins as a seemingly peaceful Tokyo is attacked by invaders while a mysterious woman (soon revealed to be Haruka) stalks Ayato. By this point, time dilation has made Haruka considerably older than Ayato and his friends who remained inside. Because of this, Ayato does not recognize Haruka and initially mistrusts her, but he gradually re-discovers his love for her as the series progresses and he learns of what has happened. At the end of the series, Ayato’s RahXephon merges with Quon’s, and he “re-tunes the world” (that is, modifies the past) so that he and Haruka are never separated. In the final sequence of the series, the adult Ayato (who can now easily be mistaken for Dr. Kisaragi, his twin brother) is seen with his wife Haruka and their infant daughter Quon.
via wikipedia
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