A.D. 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 all, Batou, who was stalking the case on a separate track, encounters Motoko. She goes away after saying, "Stay away from the Solid State Society." Batou is left with a doubt in his mind. Could Motoko be the 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...