Togusa has been released from jail. But his badge and gun are confiscated, and he's given papers showing the dissolution of Section 9. Out of work and depressed, he tries to find information on the others, but there is nothing available. Thinking that he has nothing left to lose, he goes to assassinate the man responsible when he is stopped by--Batou! It seems that Section 9 is still alive and well after all, but what about the Major?
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.