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.
Shigematsu Shizuma lives with his senile mother, his wife Shigeko, and his niece Yasuko in a village near Fukuyama. He, his wife, his niece and his close friends in the village were present at the atomic bombing of Hiroshima. The Shizumas look for prospective husbands for Yasuko, but find that the families withdraw on finding out she was at Hiroshima.