Set in the year 2027, a year following the end of the non-nuclear World War IV, a bomb has gone off in Newport City, killing a major arms dealer who may have ties with the mysterious 501 Organisation. Public Security official Daisuke Aramaki hires full-body cyber prosthesis user and hacker extraordinaire Motoko Kusanagi to investigate, but on the case with her are "Sleepless Eye" Batou who believes Kusanagi is a criminal, Niihama Prefecture Detective Togusa who is investigating a series of prostitute murders he believes are related to the incident, and Lieutenant Colonel Kurtz of the 501 Organisation who also wishes to keep an eye on Kusanagi.