"To end the war and protect my wife, I must delete you all…"

Japan, 2025. Technology has been advancing more and more rapidly.

"Brain cyberization" that makes possible direct connections to information networks via the brain, the technology of "prosthetic bodies" that allows humans to change their body parts into cybernetical ones; in this world where such scientific advances have become common, a bombing attack threat is sent to the Japanese government.

The target is an international meeting involving dignitaries from the Republic of Kuzan. The case is entrusted to the Ministry of Home Affairs' Public Security Section 9.

Section 9's leader, the full-cyborg Motoko Kusanagi, assembles her team and heads off to trap and eliminate the terrorist.