Section 9's next case is a rash of mass-kidnappings. Rumor has it that a crime syndicate is harvesting organs and selling them on the black market. As they research the case, they realize that time is running out. If they don't find the kidnapped girls soon, it will be too late. And to make matters worse, there's a Russian cyborg operative who has gone rogue and is now working for the syndicate.
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.