In the year 2034, Major Motoko Kusanagi (Atsuko Tanaka) decides to go on her own and left the Public Security Section 9. Tosuga is then promoted as a squad commander to be in charge of the new elite unit Section 9. The new appointed leader has expanded his team which includes Batou (Akio Otsuka) as well as Chief Aramaki (Osamu Saka). All of them join in to investigate a series of complicated suicide incidents. Their investigation leads them to a terrorist plot which involves micro-machines which are created to release a deadly virus. The trail leads them to a wizard hacker known as the Puppeteer. However, their investigation is stalled when they discover that someone is trying to cover up the crimes using a sophisticated attack to their computer systems.