High schoolers Mitsuha and Taki are complete strangers living separate lives. But one night, they suddenly switch places. Mitsuha wakes up in Taki’s body, and he in hers. This bizarre occurrence continues to happen randomly, and the two must adjust their lives around each other.

The story takes place in the year 2034, two years after the events in Ghost in the Shell: S.A.C. 2nd GIG. Female cyborg Major Motoko Kusanagi has left Public Security Section 9, an elite counter-terrorist and anti-crime unit specializing in cyber-warfare, which has expanded to a team of 20 field operatives with Togusa acting as the field lead.