In the year 2029, Niihama City has become a technologically advanced metropolis. Due to great improvements in cybernetics, its citizens are able to replace their limbs with robotic parts. The world is now more interconnected than ever before, and the city's Public Security Section 9 is responsible for combating corruption, terrorism, and other dangerous threats following this shift toward globalisation.
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.