Despite their best efforts, the remaining members of Section 9 are rounded up one by one by the government forces. Only Batou and Motoko are left. Batou goes to Motoko's apartment, even though he's sure its under surveillance. Once inside, he is attacked by the troops, but discovers Motoko's secret weapons cache and manages to fight back. But when the Armed Suit shows up, things start to go badly.
After being ambushed by Kuze's followers at a false location, Section 9 is alerted to his true location, and his intentions of purchasing nuclear materials from the Russian mafia.The Cabinet Intelligence Service and Gohda are involved behind the scenes.
The entire city of Nagasaki is evacuated and the JSDF moves in after a live nuclear bomb is found planted in the city, presumably by Dejima militants. Section 9 arrives to defuse the bomb and determine its precise origins.
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.