Togusa is on the trail of the Laughing Man again, and this time, his investigations lead him towards both a leading micromachine corporation and an NGO called the Sunflower Society.

The Tachikomas, Ishikawa, and Borma locate a suspicious file believed to be the Individual Eleven virus, The Major, Batou, Saito go after Kuze, and the Individual Eleven prepare to put their plan into action.

Despite close scrutiny by the authorities, the Dejima refugees declare their independence. Kuze is suspected to be the mastermind behind this new resistance and Section 9 is sent to detain him.

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.