After wrapping up the "Laughing Man" case, Section 9 is brought back into action by the newly appointed Prime Minister, Youko Kayabuki, to deal with the ongoing danger of cyber-terrorism in Japan. A group calling themselves "The Individual Eleven" begins carrying out terrorist attacks throughout the country. While Motoko Kusanagi, Daisuke Aramaki, Batou, and the rest of Section 9 look into this new threat, the government is also dealing with another major issue: refugees displaced by the Third World War are trying to enter Japan. As Section 9 conducts their investigation, they keep crossing paths with Gouda Kazundo, a high-ranking official from the Cabinet Intelligence Service, which makes them suspect he's involved. This hints that the refugee situation and the actions of The Individual Eleven might be linked in ways they hadn't considered.

In this installment

A.D. 2034. Two years have passed since Motoko Kusanagi departed from Section 9. Togusa has assumed leadership of the team, which has significantly expanded its roster of personnel. The newly enlarged Section 9 tackles a series of complex incidents, and their investigations reveal that an ultra-wizard hacker known as the Puppeteer is orchestrating the entire chain of events. Meanwhile, Batou, pursuing the case on a separate path, encounters Motoko. She leaves him with the warning, "Stay away from the Solid State Society," before disappearing. Batou is left with a lingering suspicion: could Motoko herself be the Puppeteer? The intriguing incidents confronting Section 9 gradually interconnect with an almost artistic precision. Who is the Puppeteer? What will become of Batou's relationship with Motoko? What is the complete truth behind this meticulously orchestrated perfect crime? And what will the outcome be? Mysteries surround the Solid State Society...