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 “Puppet Master” is behind the entire series of events.

The heavily cyborged police officer Batou, newly partnered with the mostly-human Togusa after the diappearance of Major Motoko Kusanagi, is assigned to investigate a series of murders committed by prototype “sexaroids” - female androids created for sex.

In the year 2029, the barriers of our world have been broken down by the net and by cybernetics, but this brings new vulnerability to humans in the form of brain-hacking. When a highly-wanted hacker known as ‘The Puppetmaster’ begins involving them in politics, Section 9, a group of cybernetically enhanced cops, are called in to investigate and stop the Puppetmaster. The pursuit will call into question what makes a human and what is the Puppetmaster in a world where the distinction between human and machine is increasingly blurry.