A certain type of android, the GA07_JL, nicknamed Jeri by its users, has been affected by a virus. Recently, all Jeri model androids have been committing "suicide". Section 9 is called in as it may be related to a virus detected in an android at the National Assembly Building.

Togusa goes undercover at a hospital for patients with Closed Cyberbrain Syndrome, a hospital completely cut off from communication with the outside world.

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.

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.

Despite their best efforts, the remaining members of Section 9 are rounded up one by one by the government forces; only Batou and Motoko are left.

Togusa has been released from jail and he's given papers showing the dissolution of Section 9. Out of work and depressed, he tries to find information on the others, but there is nothing available. Thinking that he has nothing left to lose, he goes to assassinate the man responsible when he is stopped by–Batou!

=A hacker and thief by the name of Cash Eye plans on infiltrating a vault during a party, and Section 9 is called in to prevent it. But there are a number of strange elements in this case that don't all add up.

During a scheduled maintenance, the Tachikomas begin to chat away about the Individual Eleven. While talking in their new "forum", Batou and Togusa appear and take one of the Tachikomas - who just happens to be Batou's pet - with them to Spring-8 to look at the scientific evidence gathered on the Individual Eleven.

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 Prime Minister is taken into custody, and the military begins its strike on Dejima. The Major and part of Section 9 head to Dejima to try to hand over the nuclear device to the military there, in order to defuse the situation, while Ishikawa heads to SPring-8 to deliver the rest of the plutonium.

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.