Public Security Section 9 is an elite special ops unit that works directly under the control of the Prime Minister. They've been called in to rescue a high-ranking government official from a hostage situation. But something doesn't seem right to Major Motoko Kusanagi.

Kenbishi Heavy Industries has built a state-of-the-art multiped tank. There's only one problem–it's gone haywire and started moving on its own. Section 9 is called in to stop it, as the Self Defense Force will not get involved. Now, it's up to Motoko, Batou, and the rest of Section 9 to stop the tank and figure out what made it go berserk in the first place.

As Togusa and Bato track down Nanao, Motoko and Paz are attempting to protect the Superintendent-General at a press conference about the police misuse of interceptors. When the virus does hit, Motoko and Paz have to act fast to save the intended victim. Meanwhile, the road to Nanao=A hits a dead end.

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

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!

While at an international police conference in London, Aramaki drops by to visit an old flame who's now in the wine brokering business. She asks him to help her put a stop to the corruption in her company, but he tells her that it's out of his jurisdiction. Just then, however, two thieves break into the building and take them hostage.

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.

An assassination threat has been made against Prime Minister Kayabuki; Section 9 is called to serve as bodyguards Meanwhile, investigation on the Individual Eleven turns up some interesting history.

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.

The Major and Batou are flown to Berlin in an effort to track down a terrorist called "Angel's Feathers". While there, Batou attracts the attention of a young girl in a wheelchair.

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.

The tables seem to be turning in favor of Section 9, but the nuclear missile is still being prepared for launch.