The year is 2045. As a result of the Global Simultaneous Default, an economic disaster that shook every country on Earth to its foundations, as well as the explosive evolution of artificial intelligence, the world has plunged into the Sustainable War, a planned war that can be continued indefinitely. In this near future, the decline has not yet become bad enough that people can sense in their daily lives the risk to human survival posed by A.I.

To combat cybercrimes by the Posthumans, a new breed of human being that has suddenly arisen, Public Security Section 9, led by the fully prosthetic cyborg Kusanagi Motoko, makes its way to Tokyo, which was reduced to ruins in a previous war. What they find there are a refugee group that calls itself "N" and a hostile American Special Forces unit. As the risk of nuclear war set off by a hijacked submarine grows ever greater, the three-way battle between Public Security Section 9, America, and the Posthumans intensifies.