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...

In 2030 AD, even if the intention to run around as light and electrons is concentrated in one direction as the computerization becomes generalized and the information network becomes more sophisticated, by the time the "lonely person" becomes an "individual" as a complex. Is an era when it is not computerized. It depicts the activities of the "Public Security Section 9" (commonly known as "Ghost in the Shell"), which was established as an independent counterintelligence unit under the direct control of the Ministry of Home Affairs to counter complicated crimes. There are a wide variety of top-secret missions such as cybercrime investigation, terrorism deterrence / arrest, VIP protection, and corruption detection, but one incident emerges as it is carried out.

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.

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。