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.

The story of the film is set after the conflict instigated by Toyotomi Hideyoshi ended, but not before the Battle of Sekigahara determines who shall be the Shogun of Japan.