Major Motoko Kusanagi is an elite officer in the section 9 security force: a cybernetic agent so heavily modified that little more than her Ghost remains. Along with fellow cyborg Bateau and the mostly human Togusa, Kusanagi is set on the trail of a computer-criminal known as the Puppet Master, a data theif skilled enough to hack into the very minds of his victims. His human marionettes live out existences that are nothing more than computer generated fantasy, unwittly commiting their master's crimes while the Ghosthacker hides in the darkness.

     But as Kusanagi digs deeper into the walls of secrecy surronding the case, it appears that the Puppet Master has a special interest in her alone. And when the Ministry of Foreign Affairs, a shadowy Section 6, enter the scene, Kusanagi becomes tangeled in a web of plot and counterplot, and realizes that the true identity of her invisible assailant lies at the center of a vast and lethal political conspiracy....