Motoko's friend Courtin asks her to come to the hospital where she works. It seems a little girl just received a heart transplant, but the donor's family doesn't remember ever agreeing to donate the heart. Seeing the little girl reminds Motoko of her own past. When she mentions this story to Aramaki, he tells them to determine if this is tied to a ring of black-market organ smugglers supposedly run by the mafia.
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.