While at an international police conference in London, Aramaki drops by to visit an old flame who's now in the wine brokering business. She asks him to help her put a stop to the corruption in her company, but he tells her that it's out of his jurisdiction. Just then, however, two thieves break into the building and take them hostage. With a corrupt police official on the outside, it's up to Aramaki to keep them alive and buy enough time for the Major to figure out what's going on.
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.