In a futuristic Japan recovering from a devastating world war, cutting-edge cybernetics offer a chance to extend life and alleviate suffering. Society is interconnected through a unified system called 'ghosts', but faces a grave threat from cyber terrorists who can manipulate bodies and memories. When a dangerous virus named Fire-Starter infiltrates the system, resulting in the Prime Minister's assassination, Major Motoko Kusanagi and her expert team are tasked with identifying its origin. As they probe deeper, they stumble upon signs of governmental misconduct and encounter a mysterious figure with a strikingly familiar identity.