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.

In this prequel set one year after the fourth World War, cyborg and hacker extraordinaire Motoko Kusanagi from the military's 501st Secret Unit finds herself wrapped up in the investigation of a devastating bombing.