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. The two groups rival each other in a case involving a man who receives false memories of a refugee transport operation.
Set in a futuristic Japan after the end of a brutal world war, science has advanced by leaps and bounds giving humanity the choice to prolong life and reduce suffering with the use of sophisticated cybernetics. With all of humanity linked into one system of minds and personalities known as ghosts, the biggest threat to civilization is the cyber terrorists capable of hijacking people's bodies and memories. 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. As they delve deeper and deeper into their investigation, they uncover traces of government corruption and a shadowy broker that bears an all-too-familiar face. The film is a continuation to the plot of the Pyrophoric Cult episode of Arise, and ties up loose ends from that arc.
A short movie with Motoko Kusanagi explaining the move from the Ghost in the Shell website kokaku-a to the top level domain '.jp'