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。

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.

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...