The story continues to follow the adventures of Section 9's top members, Motoko Kusanagi, Batou, and Togusa. For this second season, Innocence-famed director Mamoru Oshii contributed with his ideas to the concept of the entire series right from the initial planning stages. 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. The in-depth storytelling of the series is likely to surpass the first series.

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Prequel: Koukaku Kidoutai Stand Alone Complex
Summary: Koukaku Kidoutai S.A.C. 2nd GIG: Individual Eleven
Sequel: Koukaku Kidoutai Stand Alone Complex: Solid State Society