In 2027, a year after the fourth non‑nuclear war concluded, the anime"s narrative takes place. New Port City remains in recovery when a self‑propelled mine detonates, unleashing a catastrophic bombing that leaves the streets in ruin. Soon after this disaster, a military officer who had been implicated in clandestine arms‑dealing bribes is gunned down, sparking a tense investigation.
During the probe, Public Security Section agent Daisuke Aramaki encounters Motoko Kusanagi, a hacker serving in the army"s 501st Secret Unit. Batou—known for his "always‑watching" eye that never sleeps—convinces himself that Kusanagi orchestrated the explosion. Meanwhile, Niihama Prefectural Police detective Togusa is juggling two cases: the officer"s shooting and a prostitute"s murder. Kusanagi herself remains under close scrutiny by Unit commander Kurutsu and other cyborg agents.