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.

The year is 2030. Six months passed since the Laughing Man Incident was solved. About 3 million refugees are living in Japan, invited to fill the labor shortage. However, the emergent presence of the invited-refugees intensified their confrontation with the "Individualists", who called for national isolation, which then led to the increased incidences of terrorist attacks. Under these circumstances, a terrorist group called the Individual Eleven carries out a suicide attack. But there was a greater scheme behind their action. When Section 9 learns this, they attempt to nail down the mastermind of the incident. Meanwhile, Kuze, a surviving member of the Individual Eleven, becomes a charismatic leader of the invited-refugees and intensifies the confrontation against the government. And Motoko starts feeling a strange sense of fate connecting her with Kuze...

The year is 2030 and six years have passed since a criminal known only as "The Laughing Man" swept through top medical nanotechnology firms committing acts of cyber-terrorism, kidnapping, and espionage leaving no known suspects. New information is revealed, as Section 9 enters the hunt for a suspect capable of unfathomable actions in this compilation of Stand Alone Complex content.

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.