In the year 2029, Section 9, a group of cybernetically enhanced cops, are called in to investigate and stop a highly-wanted hacker known as 'The Puppetmaster'. Ghost in the Shell 2.0 is a reproduced version of its original 1995 counterpart. Among a numerous enhancements, for the film's 2.0 release, were a number of scenes were overhauled with 3D animation, visual improvements, and soundtrack rerecorded in 6.1 surround sound.

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.

Cyborg detective Batou is assigned to investigate a series of murders committed by gynoids—doll-like cyborgs, which all malfunctioned, killed, then self-destructed afterwards. The brains of the gynoids initialize in order to protect their manufacturer's software, but in one gynoid, which Batou himself neutralized, one file remains: a voice speaking the phrase "Help me."