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."

笑脸男事件结束后，公安9课新的敌人是自称“个人的11人”的反政府武装组织。在其计划周密的犯罪背后，牵扯的战争难民问题更令整个社会的矛盾激化。面对政府与犯罪分子带来的压力，草薙素子再次带领公安9课出动。

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.