A.D. 2034. It has been two years since Motoko Kusanagi departed Section 9. Togusa now leads the team, which has significantly expanded its roster. The enlarged Section 9 tackles a wave of complex incidents, and investigations uncover that an ultra-wizard hacker known as the Puppeteer is responsible for the entire sequence of events. Amidst this, Batou, who has been pursuing the case on a separate track, runs into Motoko. She leaves after warning, "Stay away from the Solid State Society." Batou is left with a lingering doubt. Could Motoko be the Puppeteer? The series of intriguing incidents facing Section 9 gradually connect in an almost artistic manner. Who is the Puppeteer? What will become of Batou's relationship with Motoko? What is the complete truth behind this meticulously planned perfect crime? And what will the result be? Mysteries envelop the Solid State Society...