2032년 해체 위기에 놓인 공안9과, 즉 공각기동대는 테러리스트 '개별의 11명(Individual Eleven)' 사건을 발단으로 해체 위기를 넘긴다. 쿠사나기 모토코를 비롯한 공안9과가 사건을 파고 들자 내각정보청의 음모가 점점 모습을 드러낸다. 시로 마사무네 원작 만화 를 바탕으로, 이후 제작된 TV 시리즈 2기. 감독 오시이 마모루가 스토리 컨셉에 참여.

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…