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. When Motoko 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.

The Major has become worried about the Tachikomas. It appears that their AIs have developed much more quickly and in ways that were not anticipated; they have begun speaking about their "individuality".

Batou goes undercover on a military base to shadow one of his former heroes, a man named Zaitsev who was an Olympic silver medalist. Now, however, he's under suspicion of espionage. Batou befriends him easily, and the two really seem to get along--which is unusual for Batou. But when Batou learns the truth behind his hero, he must make a very difficult decision.

After being shot, Togusa's in the hospital and about to go into surgery, but he is desperate to pass on what he's learned to the rest of Section 9. As Togusa fights for his life, the rest of Section 9 takes over the case, but others within the government have learned of the investigation and are not happy.

While on a stakeout of a Taiwanese vegetarian restaurant, Section 9 finds out that someone is pulling strings and feeding misinformation to the Public Safety Sections.

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

Section 9 heads to Etorofu in search of Kuze. During their investigations, the Major finds an interesting floppy disk on the body of a dead addict.

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.

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.