A.D. 2034: It has been two years since Motoko Kusanagi 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 Master 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 Puppeteer?