For the films Version 2.0 release, all the original animations were re-produced with latest digital film and animation technologies, such as 3D-CGI. The original soundtrack was also re-organized and re-recorded. he movie begins with Major Motoko Kusanagi spying on a meeting taking place in New Port City. The meeting is interrupted by a Section 6 enforcement team, at which point Motoko kills a foreign diplomat in the meeting who is attempting to transport an important programmer out of the country.

In the next scene, Section 9 chief Daisuke Aramaki is introduced conversing with an official about programmers who are attempting to gain political asylum. The story then moves into the main plotline when Aramaki describes one of the minister's interpreters having had her brain hacked into by the mysterious "Puppet Master".