AD 2034. It has been two years since Kusanagi Motoko left Section 9. Togusa is now the new leader of the team, that has considerably increased its appointed personnel. The expanded new Section 9 confronts a rash of complicated incidents, and investigations reveal that an ultra-wizard hacker named the Puppeteer is behind the entire series of events.

In the midst of it all, Batou, who was following the case on a separate track, encounters Motoko. But after saying, "Stay away from the Solid State Society", she quickly leaves. This makes Batou wonder: Could Motoko be the Puppeteer?

The series of intriguing incidents that Section 9 faces gradually link together — almost artistically. Who is the Puppeteer? What will happen to Batou's relationship with Motoko? What is the full truth behind this carefully planned perfect crime? And what will the outcome be? Mysteries surround the Solid State Society...