After the conclusion of the "Laughing Man" case, Japan's newly appointed Prime Minister, Youko Kayabuki, reinstates Section 9 to combat cyber-terrorism. A group known as "The Individual Eleven" has started committing acts of terror throughout Japan. Motoko Kusanagi, Daisuke Aramaki, Batou, and other members of Section 9 investigate this new threat while the Japanese government faces a separate crisis: refugees from the Third World War seek refuge in Japan. However, as they pursue Gouda Kazundo, a high-ranking member of the Cabinet Intelligence Service, they begin to suspect that he may be involved and that the events surrounding the refugee crisis and The Individual Eleven are more connected than they initially thought.