During a raid on a meeting with a foreign representative that he suspects involves corruption and criminal activity, Public Security's Daisuke Aramaki encounters a mysterious cyborg. Introducing herself as Motoko Kusanagi, the cyborg proposes the formation of a new special forces unit to the Minister of Internal Affairs. Aramaki asks Kusanagi to investigate something as a first step.
Kusanagi and her team begin operating as the Ghost in the Shell unit after being scouted by Aramaki. One day, a virus infiltrates the cyberbrain of the Foreign Minister's interpreter. Sensing that Colonel Mares, who is in exile, is trying to disrupt a secret meeting, Aramaki instructs Kusanagi and the others to track down the culprit using reverse tracking.
After a fierce chase involving the Fuchikoma, Kusanagi and Togusa apprehend the suspect. Meanwhile, while Aramaki and Batou stake out the location, the unidentified hacker known as "The Puppet Master," who is suspected to be the one who planted the virus, makes an appearance at Colonel Mares's location.
There has been a rash of attacks against humans by promotional sample robots. Kusanagi's team rounds up robots of that same model line, and they learn that they all share a common trait. Batou and Togusa head to Hanka Precision Instruments, where they are made, to determine what is behind the attacks.