A Japanese police unit who use giant anthropomorphic robots (called Labors) is caught up in a political struggle between the civilian authorities and the military when a terrorist act is blamed on an Air Force jet. With the aid of a government agent, the team gets close to a terrorist leader to stop things from going out of control when after the military is impelled to impose martial law.

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."

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.