It is 2027, a year after 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 had ties with the mysterious 501 Organization. Public Security official Aramaki Daisuke hires full-body cyber prosthesis user and hacker extraordinaire Kusanagi Motoko to investigate. Working on the case with her are: "Sleepless Eyes" Batou, who believes Motoko is a criminal; Niihama Prefecture Police Detective Togusa, who is investigating a series of prostitute murders he believes are related to the incident; and Lieutenant Colonel Kurutsu of the 501 Organization, who also wishes to keep an eye on Motoko. Meanwhile, bits of the past of the members of this new Public Security organization, Section 9, begin to surface.