After being shot, Togusa's in the hospital and about to go into surgery, but he is desperate to pass on what he's learned to the rest of Section 9. As Togusa fights for his life, the rest of Section 9 takes over the case, but others within the government have learned of the investigation and are not happy.

The government orders Section 9 disbanded. Aramaki is taken away, and Togusa is arrested. Motoko assembles the remaining team members at HQ for one final mission. They prepare for a full-scale assault while Elite troopers and Armed Suits descend on Section 9 HQ.

A group of terrorists identifying themselves as the "Individual Eleven" barricade themselves within the Chinese Embassy. Section 9 is called in to eliminate the terrorists without any civilian casualties, all before the scheduled police raid.

The government declares martial Law in Dejima, believing that the refugees have a nuclear device and plan to use it to gain independence. When the refugees' connection to Kuze is cut off, one shot begins a bloody war.