Female cyborg Major Motoko Kusanagi and her fellow police officers of Section 9 hunt down a host of criminals in both the real and online worlds. In the course of their work, Kusanagi and Section 9 must do everything from resolving hostage crises to hunting down runaway state-of-the-art killing machines.

The story continues to follow the adventures of Section 9's top members, Motoko Kusanagi, Batou, and Togusa. The series maintains an episodic format and portrays Section 9 dealing with political issues such as invited refugees and nuclear intrigue. Another government institution, the Information Bureau of the Cabinet, comes up head-to-head against them. And a terrorist entity who calls itself the "Individual Eleven" joins the set.