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 Shell Squad after being scouted by Aramaki. At some point, the cyberbrain of the Foreign Minister's interpreter was infected by a virus. Aramaki senses that Col. Malles, who is living in exile in the country, is trying to interfere with a secret meeting. He orders Kusanagi to back-trace the hack and find the culprit.

Kusanagi and Togusa take their suspect into custody after a furious chase in their Fuchikomas. Elsewhere, Aramaki and Batou are staking out Col. Malles when he is paid a visit by someone they suspect is the Puppet Master, the hacker who released the virus on his orders.

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.