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

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.

A group of terrorists identifying themselves as the "Individual Eleven" barricade themselves within the Chinese Embassy. Section 9 is called in to eliminate the terrorists without any civilian casualties, all before the scheduled police raid.

=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.

A seemingly run-of-the mill hit-and-run turns into anything but when Togusa investigates. While in Tokyo, he discovers a secret from the past the GSDF is trying to keep hidden deep underground.

The Tachikomas, Ishikawa, and Borma locate a suspicious file believed to be the Individual Eleven virus, The Major, Batou, Saito go after Kuze, and the Individual Eleven prepare to put their plan into action.

The Prime Minister is alerted to the existence of "hub cyberbrains," while Ishikawa returns from the peninsula to report on what he found out about Kuze's past.

Despite close scrutiny by the authorities, the Dejima refugees declare their independence. Kuze is suspected to be the mastermind behind this new resistance and Section 9 is sent to detain 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.

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.