A cyborg policewoman and her partner hunt a mysterious and powerful hacker called the Puppet Master.

In 1930s Berlin, a gay Jew is sent to a concentration camp under the Nazi regime.

Motoko and Batou work to try to stop a terrorist organization whose symbol is the Scylla. Meanwhile, Togusa investigates a murder of a man who possessed a prosthetic leg manufactured by the Mermaid's Leg corporation.

When the riot squad starts shooting citizens during the holiday season, the Major and her team must track down a terrorist hacker who operates under the name Fire-Starter.