Motoko and her squad are finally getting closer to Fire-Starter's broker, but things get tense when they're instructed to take a backseat role on a sting operation.

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.

Motoko and Public Security Section 9 must track down a terrorist known as “Fire Starter”, who unleashes an infection that affects cyberbrains.

The anime's story is set in 2027, one year after the end of the fourth non-nuclear war. New Port City is still reeling from the war's aftermath when it suffers a bombing caused by a self-propelled mine. Then, a military member implicated in arms-dealing bribes is gunned down. During the investigation, Public Security Section's Daisuke Aramaki encounters Motoko Kusanagi, the cyborg wizard-level hacker assigned to the military's 501st Secret Unit. Batou, a man with the "eye that does not sleep," suspects that Kusanagi is the one behind the bombing. The Niihama Prefectural Police detective Togusa is pursuing his own dual cases of the shooting death and a prostitute's murder. Motoko herself is being watched by the 501st Secret Unit's head Kurutsu and cyborg agents.

Freed of her responsibilities with the 501 Organization, Motoko Kusanagi must now learn how to take orders from Aramaki. Someone hacks the Logicomas, and Batou enlists the help of former army intelligence officer Ishikawa and former air artillery expert Borma. Kusanagi also seeks to enlist ace sniper Saito and undercover cop Paz into the new Public Security Section 9.

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.