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.  

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.