With Major Motoko Kusanagi missing, Section 9's Batou is tasked with investigating a series of gruesome murders—apparently committed by malfunctioning gynoids, or sex robots. However, when a defective gynoid leaves Batou a cryptic message, he starts to doubt the cause of their malfunctions. Suspicions of politically motivated killings and an illegal "ghost" soon arise, pulling Batou and his partner Togusa into a dangerous web of conspiracy. As the investigation continues, the boundary between human and machine grows increasingly blurred, making reality and perception indistinguishable. Facing strange and dangerous adversaries, Batou and Togusa navigate a futuristic world populated by machines and living dolls, yet completely lacking in humanity.