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.

Youngsters called Kildren, who are destined to live eternally in their adolescence. The Kildren are conscious that every day could be the last, because they fight a war as entertainment, organized and operated by adults. But as they embrace the reality they are faced with, they live their day-to-day lives to the full.