After the resolution of the "Laughing Man" case, Japan's newly appointed Prime Minister, Youko Kayabuki, resurrects Section 9 to combat the growing threat of cyber-terrorism. A group of terrorists called "The Individual Eleven" emerges and creates chaos throughout the country. As Section 9, led by Motoko Kusanagi and Daisuke Aramaki, investigates the case, the Japanese government is dealing with another predicament - a surge of foreign refugees seeking asylum after the Third World War. However, the investigation reveals Gouda Kazundo, a high-ranking agent of the Cabinet Intelligence Service, as a suspicious character, leading Section 9 to suspect that the refugee situation may be connected to The Individual Eleven.