The year is 2034, and the face of terrorism has changed. No longer restricted to the limits of the physical world, the war on terror has exploded on the net. In an attempt to confront this new threat, an elite counter-terrorism and anti-crime unit was formed: Public Security Section 9. Two years have passed since the team's commander, Major Motoko Kusanagi, resigned from her post. After a rash of mysterious suicides, Section 9 is forced to confront the "Puppeteer," a dangerous hacker with unsurpassed skills. As their investigation of this terrorist threat takes them deeper into the bowels of a potential government conspiracy, Section 9 once again crosses paths with the Major, but is her sudden reappearance no more than a coincidence, or is she somehow connected to the "Puppeteer"?