In the year 2045, after an economic disaster known as the Synchronized Global Default, rapid developments in AI helped propel the world to enter a state of "sustainable war", but the threat of human extinction at the hands of AI hasn't yet pervaded the public consciousness.

Former members of Public Security Section 9, including full-body cyborg Major Motoko Kusanagi, are working as hired mercenaries when mysterious beings known as "post humans" begin to emerge. When the world's superpowers are trying to come to grips with the threat, the members of Section9 comeback together again in order to face this new threat.