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. The story reveals that two floating cities appeared above Tokyo and Sendai around the beginning of 2013. The ensuing conflict escalated into nuclear warfare, and the Mu enveloped Tokyo and outlying suburbs within a spherical barrier resembling Jupiter, referred to as "Tokyo Jupiter" by all those outside. The barrier has a dilatory effect on time, with time inside Tokyo Jupiter passing about one-sixth as fast as the outside time.

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