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.
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 Prime Minister is taken into custody, and the military begins its strike on Dejima. The Major and part of Section 9 head to Dejima to try to hand over the nuclear device to the military there, in order to defuse the situation, while Ishikawa heads to SPring-8 to deliver the rest of the plutonium.
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.