Motoko is asked by her friend Kurutan to investigate a strange scenario. A six-year old girl's life was saved by an immediate heart transplant. When her parents tried to send their gratitude to the donor, the donor's parents filed a police report since they never gave permission for the donation.

What's more, the investigating officer has now been hospitalized after an accident. There is more to this case then meets the eye and Motoko and her colleagues must find out who's behind these apparent illegal organ donations.

Following a tip, the Major conducts an undercover investigation of Kuze in Taiwan. While there, she saves a boy running from the Mafia.

After being saved, the boy follows her, making sure that she finishes what she started. The mafia will continue to pursue the boy and the Major has to protect him.

The city of Fukuoka is evacuated when a live nuclear bomb is found. With the Dejima Refugees targeted as the prime suspects, the government sends the Self-Defense Forces into the city.

Aramaki suspects the CIS's involvement in this latest incident is deeper then it appears. Batou is sent to gather more information from Gouda, but will he be able to hold his temper against the arrogant agent?