Yutaka Nakano

The war between the Levamme Empire and the Amatsukami Imperium has been raging for years. In the midst of this struggle, the prince of the Levamme Empire declares his love for Juana del Moral and vows to end the war in one year, as part of his marriage proposal. When the Amatsukami catch wind of this, they assault the del Moral residence, targeting Juana's life. As a last-ditch effort to bring the prince his bride, the San Maltilia Airforce employs a mercenary of mixed blood—a bestado—to fly Juana to the prince in secret.

The story takes place in the year 2034, two years after the events in Ghost in the Shell: S.A.C. 2nd GIG. Female cyborg Major Motoko Kusanagi has left Public Security Section 9, an elite counter-terrorist and anti-crime unit specializing in cyber-warfare, which has expanded to a team of 20 field operatives with Togusa acting as the field lead.

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.