A recent string of murders perpetrated by a prototype female android has drawn the attention of Section 9, a unit specializing in counter cyber-terrorism. With none of the victims' families pressing charges, suspicions arise regarding the nature of the androids and their production. Investigative duties fall to cyborg commando Batou and his newly recruited biological partner, Togusa. Can the two overcome their differences and discover the truth behind this string of murders?

A.D. 2034. It has been two years since Motoko Kusanagi left Section 9. Togusa is now the new leader of the team that has considerably increased its appointed personnel. The expanded new Section 9 confronts a rash of complicated incidents, and investigations reveal that an ultra-wizard hacker nicknamed the "Puppeteer" is behind the entire series of events.

Uprisings over the treatment of a wave of Asian immigrants threaten the political landscape, and the new Prime Minister brings in Section 9 to offer their services - but on a much tighter leash than they're used to. After being reinstated, they must stop an assassin who is killing high-ranking officials, outmaneuver an incredibly talented thief, and unravel the reason a high-tech helicopter malfunctioned. And all under the supervision of the mysterious and disturbing man known as Gohda.

On her first visit to one of the refugee areas, the Prime Minister receives a bouquet of flowers with a death threat in it. Section 9 is called in to provide round-the-clock security for her as they work to catch the would-be assassin. As they do their legwork, more and more links to the mysterious "Individual Eleven" are uncovered.

After their prior confrontations with Gohda, Section 9 continues their investigations into the man and his mysterious background. At the same time, they must stop a wave of suicide bombers who threaten the peace and safety of Japan. And even when they're off duty, trouble manages to find them, as Togusa finds himself brought up on charges for actions he took while off duty.

While on the trail of Kuze, Section 9 tracks down the person who made his one-of-a-kind prosthetic face. There's only one problem - the designer is dead. And the person who killed his is Paz, or someone who looks exactly like him! This special edition includes a collectible tin case, two figures, and the second original 2nd Gig soundtrack.

The Major, following a lead on Kuze, the lone member of the Individual Eleven who survived, heads to Taiwan. There, she becomes involved in some local "trouble" involving a kid and the local gangs. Then, inexplicably, Batou and the Major are assigned to an international task force to capture the terrorist Angel's Wing. And while they're halfway around the world in Berlin, Section 9 continues their investigation.