Kusanagi and her boyfriend are rushed to the hospital after being attacked without warning. They suspect Toru Soma, a terrorist that Kusanagi has a history with. Kusanagi and Togusa leave the hospital, and after leading their pursuers on a chase, they find themselves in a fierce battle against an armed group in an abandoned factory.

Kusanagi's team surveils cyborg Koil Krasnov. To expose corruption behind Sagawa Electronics' factory expansion, Kusanagi infiltrates their offices while Batou heads to the factory.

Promotional sample robots attack humans. Kusanagi's team rounds up robots from that model line and discovers they share a common trait. Batou and Togusa go to Hanka Precision Instruments to find what's behind the attacks.

After a high-speed chase led by the Fuchikomas, Kusanagi and Togusa take the suspect into custody. Aramaki and Batou are monitoring the situation, the hacker known as 'Puppet Master', suspected of having introduced the virus.

Kusanagi's Shell Squad, recruited by Aramaki, investigates when a virus infects the Foreign Minister's interpreter's cyberbrain. Aramaki suspects exiled Col. Malles is disrupting a secret meeting and orders Kusanagi to trace the hack.

Daisuke Aramaki raids a suspected corrupt meeting and meets cyborg Motoko Kusanagi. She proposes creating a special forces unit to the Minister of Internal Affairs. Aramaki assigns her an investigation as a first task.