Assigned to investigate a series of gruesome murders that appear to be caused by faulty gynoids, Batou of Section 9 is in a predicament as Major Motoko Kusanagi is nowhere to be found. However, when a cryptic message is left for Batou by a faulty gynoid, he begins to contemplate the reason behind their malfunctioning. This leads to the emergence of theories about politically motivated murder and an illegal "ghost," drawing Batou and Togusa, his partner, into a hazardous web of conspiracy. As their investigation deepens, the line between man and machine becomes increasingly blurred, and the distinction between reality and perception fades away. Battling dangerous and strange enemies, Batou and Togusa embark on an adventure into a futuristic world replete with machines and living dolls, albeit desolate of humanity.