While tensions rise in the Dejima refugee camp, the Major hacks the refugee cyberbrain hub to determine Kuze's location.
Kuze escapes and Section 9 suffers heavy damages from the confrontation; Kuze leaves for Nagasaki harbor with the Russian package.
One of the Tachikomas decides to take a little stroll through the city. It meets a little girl, Miki, who is searching for her lost dog and it agrees to help her. On their journey, the Tachikoma finds a strange box. After the adventure with Miki is over and the Tachikoma returns home, the members of Section 9 discover the box, and find that within it is a movie theater that contains the Ghosts of all those who saw the movie. Will Motoko be the next victim?
In a briefing, Aramaki shows a photo of a girl who looks like Eka Tokura, the daughter of Tokura Electronics, who was kidnapped 16 years ago. But there's one problem--the photo was taken two days ago! When a team of special operatives was sent in, all contact was lost. Section 9 is assigned to go in and determine what's really going on.
The Chinese government contacts Section 9 to let them know that an assassin may have entered Japan to kill a famous reclusive millionaire. Despite their considerable efforts, however, Section 9 is unable to contact him to warn him, so they go directly to his residence. Unfortunately, a female cyborg assassin named Fem has arrived first. Now it's a showdown between the Major and Fem, and a man's life hangs in the balance.
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". Worried, the Major calls Batou to a meeting; the Tachikomas, having suspicions of their own, attempt to eavesdrop on their conversation. What will be the fate of Section 9's Tachikomas?
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.