Kuze manages to take down the jamming plane, but becomes trapped in rubble with the Major. The Tachikomas begin discussing what to do about the nuclear submarine they have spotted, and Batou manages to convince the special forces that have been sent to kill them to listen to him.
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.