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 Organization. Public Security official Daisuke Aramaki hires full-body cyber prosthesis user and hacker extraordinaire, Motoko Kusanagi, to investigate.

Centered on the character of Goemon, this film is a sequel to the spin-off TV series, The Woman Called Fujiko Mine and its sequel film, Daisuke Jigen's Gravestone.

In this prequel set one year after the fourth World War, cyborg and hacker extraordinaire Motoko Kusanagi from the military's 501st Secret Unit finds herself wrapped up in the investigation of a devastating bombing.