The movie begins with a flashback scene of Motoko and her best friend, Emily, as children. In the present day, Motoko and Batou go undercover as a couple on vacation in order to track down a terrorist group known as Fire Starter, whose symbol is the Scrasath.
As they investigate, they discover that Fire Starter is planning a large-scale attack on the city, and Motoko is confronted with the fact that she may have a personal connection to the group. Meanwhile, Togusa investigates the murder of a man who possessed a prosthetic leg manufactured by the Mermaid's Leg corporation, which raises questions about the company's involvement in criminal activities.
Motoko and Batou eventually uncover Fire Starter's plan to release a deadly virus, and they race against time to stop them before it's too late. Along the way, they must also confront their own pasts and personal demons.
The movie features stunning animation and action-packed scenes, as well as exploring deeper themes about identity, memory, and the impact of technology on humanity.