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.

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.

The Laughing Man returns! And, just as he did six years ago, he kidnaps the president of Serano Genomics without being detected. Section 9 arrives at Serano's house too late, and sets out to find him.

=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.

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.

While field testing new recruits, the Major finds herself hacked, and an old woman tells her a story from her past.

With the latest Individual 11 incident still fresh in the public's mind, Section 9 discovers that only a skilled face sculptor could have created Kuze's prosthetic face. Since only two artists fit that description, they quickly locate the craftsmen and go to question them.

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.

The government declares martial Law in Dejima, believing that the refugees have a nuclear device and plan to use it to gain independence. When the refugees' connection to Kuze is cut off, one shot begins a bloody war.