In a futuristic world where cybernetic bodies have become commonplace, a mysterious hacker known as the Puppet Master wages cyber warfare, hacking into the minds of unsuspecting victims and manipulating them to commit crimes. Against this backdrop, Major Motoko Kusanagi, a cyborg operative for the elite Section 9 security force, leads a team to track down and capture this elusive hacker. Her own body fully enhanced with prosthetic parts, Kusanagi navigates a space where the lines between human and machine, physical and digital reality, are blurred.

As the investigation deepens, Kusanagi and her team uncover a complex web of political intrigue and corruption involving not just the Puppet Master but the very nature of consciousness and identity. She becomes increasingly introspective, questioning her own existence and what it means to have a soul, especially as her human essence seems encased within an artificial shell. The quest to apprehend the Puppet Master becomes much more than a simple manhunt, pushing Kusanagi to confront philosophical dilemmas about self and the synthetic body.