In the near future, following the end of World War IV, a bomb has gone off in Newport City, killing a major arms dealer who may have ties with the mysterious 501 Organization. Public Security official Daisuke Aramaki hires full-body cyber prosthesis user and hacker extraordinaire, Motoko Kusanagi, to investigate. After extricating herself from the 501 Organization, Motoko Kusanagi soon must learn how to take orders from Aramaki. When unknown forces hack the Logicomas, Kusanagi enlists Saito, an ace sniper, and Paz, an undercover cop.