Following the resolution of the 'Laughing Man' case, Section 9 is reinstated under the leadership of Japan's newly elected Prime Minister, Youko Kayabuki, to combat the ongoing threat of cyber-terrorism. A new group known as 'The Individual Eleven' emerges, instigating acts of terror throughout Japan. As Motoko Kusanagi, Daisuke Aramaki, Batou, and the rest of Section 9 delve into this fresh danger, the Japanese government grapples with a separate challenge: an influx of foreign refugees seeking sanctuary after the Third World War. Amidst their pursuit, the team encounters Gouda Kazundo, a prominent figure from the Cabinet Intelligence Service, raising suspicions of his involvement and hinting at deeper connections between the refugee crisis, The Individual Eleven, and sinister forces at play.