The 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.

Posing as lovers on vacation, Motoko and Batou work to try to stop a terrorist organization whose symbol is the Scrasath. Meanwhile, Togusa investigates a murder of a man who possessed a prosthetic leg manufactured by the Mermaid's Leg corporation.

The upcoming installment's story takes place amidst signs of postwar reconstruction in the winter of 2028. Tensions are rising in New Port City as demonstrations are held concerning the interests of foreign cartels. This leads to a shooting incident involving riot police. It all started with a cyberbrain infection released by the terrorist "Fire Starter." An independent offensive unit led by Makoto Kusanagi entrusts the suppression of the situation to their ghosts and aims for their own justice. Below the surface of the incident, lies the "tin girl" Emma and the "scarecrow man" Burinda Junior. As Kusanagi deals with the incident, she draws near to what those two ghosts were seeking.

When a ghost-infecting virus known as Fire-Starter begins spreading through the system resulting in the assassination of the Japanese Prime Minister, Major Motoko Kusanagi and her elite team of special operatives are called in to track down its source.