Motoko Kusanagi doesn't need saving, but the country does, and Section 9 has to decide if a refugee crisis manufactured by the government deserves a bullet or a negotiation. The Individual Eleven aren't the plot, they're the symptom: a series of suicides that ask whether a ghost in the machine can be political, whether desperation can be contagious across networked minds. Kenji Kamiyama builds a conspiracy that doesn't resolve cleanly because the real conspiracy never does, and Yoko Kanno's score moves through it all like someone already mourning what hasn't died yet.

After the Laughing Man case is closed, Japan's new Prime Minister, Youko Kayabuki, brings Public Security Section 9 back to fight ongoing cyber-terrorism. A string of similar attacks carried out by separate suicidal groups calling themselves "The Individual Eleven" becomes the team's main focus. At the same time, the government struggles with a wave of foreign refugees displaced by the Third World War who are seeking asylum, and the threat of war grows. As Motoko Kusanagi, Daisuke Aramaki, Batou and the rest of the unit investigate, they keep running into Gouda Kazundo of the Cabinet Intelligence Service. They begin to suspect he is involved, and that the refugee crisis and the attacks may be linked. The season mixes action, mystery and psychological science fiction.