An insect-like single-seat helicopter glides over a high-rise city under the cover of night. Below, Batou navigates through a crowded street until he arrives at a crime scene. Police inform him that a suspect has taken the lives of two officers. Clutching his shotgun, Batou bravely enters a dark alley alone, where he discovers the bodies of the slain police officers and encounters a mysterious female figure sitting quietly. She suddenly attacks him, but Batou easily subdues her. As she whispers, "Help me," he realizes she is a cyborg.
The story unfolds with a striking title sequence that illustrates the stylized birth of a cyborg. Within Section 9, a briefing reveals a concerning pattern of eight recent homicides tied to the Locus Solus #2052 "Hadaly" type gynoids, each of which has self-destructed. Aramaki explains that Section 9 has assumed responsibility for the case due to the involvement of high-profile victims, including a politician and a retired public servant, suggesting possible ties to terrorism. He instructs Batou and Togusa to investigate the gynoids while Ishikawa and Azuma delve into background checks.
In the car, Togusa and Batou discuss the absence of the Major Kusanagi. Their next stop is the police forensics lab, where they encounter a weary cyborg technician, Miss Haraway, who has been analyzing the captured gynoid from the alley. Miss Haraway speculates about the gynoids' troubling ability to override their moral code, designed to prevent them from harming humans, and discusses the concept of robot suicide. She reveals that these gynoids, deemed "sexaroids," possess organs that do not serve a practical purpose, shedding light on the families of the victims who have opted for settlements. Intriguingly, the brain of the alley-gynoid was cleared except for the audio phrase "help me."
As they strategize their next move, the Section 9 dispatcher alerts them to a new 602 call concerning the Locus Solus inspector found dead at a boathouse. Upon arrival, they find Ishikawa already on the scene. The body belongs to Jack Volkerson, aged 54, who had been missing for five days. The gruesome scene highlights blood splatters in the kitchen sink and bathroom. Batou discovers a 3D photo of a young girl, prompting a grim exit just as the forensic CSI team arrives.
Later, Ishikawa drives Batou home. They pause to buy dog food, where Ishikawa reassures Batou that dry food is a better option. Batou misleads him about the location of his apartment. Upon entering his flat, he is welcomed by a playful basset hound. Batou takes time to prepare a meal for his dog, savoring a moment of peace with a cold beer.
Within Section 9, the forensic report on Volkerson reveals that he had met a violent end—his neck was broken before dismemberment. A deformed doorknob at the scene suggests the presence of an illegal cybernetic hand. Adding to the intrigue, a car linked to the local yakuza group "Kojinkai" was discovered nearby, hinting at a potential revenge motif, since one gynoid had already slain the previous head of the Kojinkai. Aramaki instructs Batou and Togusa to keep their investigation going while the rest of the team returns to routine work. In a moment of concern, Aramaki subtly requests Togusa to monitor Batou's emotional state.
In the garage, Batou preps heavy firepower for their ongoing mission. Concerned, Togusa advises a non-confrontational approach with the yakuza. Upon reaching the Kojinkai club, tension escalates as Batou demands to see the new leader, Wakabayashi. A standoff erupts when gangsters draw weapons, but Batou is quicker, dispatching them with ruthless efficiency. After a brutal firefight, they ascend to confront the leader and a cyborg with a mutant claw. Batou easily overpowers the mutant, leaving a terrified Wakabayashi to reveal that Locus Solus hinted at Volkerson's whereabouts, though he remains oblivious to the former leader's dealings with the robot company. Aramaki later lightly reprimands them for their vigilante-style approach.
Togusa drops Batou off at his favored mini-mart, where a mysterious figure forewarns him of a kill zone. Tension escalates as gunfire erupts, resulting in multiple wounds to Batou, impairing his cyber vision. Fortunately, Ishikawa arrives, reconnecting a pistol grip to Batou's neck. In the Section 9 lab, Batou awakens sporting a new arm, having been hacked and forced to harm himself. Ishikawa and Togusa arrive with Batou's pet basset hound, whom he had frequented the store for, as it was the only place selling the special dog food.
With their next destination set towards the Northern Frontier, the duo boards a VTOL craft headed for an industrial city reminiscent of a crumbling, lawless haven. Upon landing at an old cathedral, Batou and Togusa search for an informant named Lin to inquire about a former military electronics expert named Kim. They enter a luxurious mansion and discover disturbing imagery before prowling upstairs, encountering a corpse-like cyborg. A fast realization about the body being a ruse leads Batou to confront Kim, who cryptically narrates the production of gynoids aboard a factory ship.
Haunting philosophical exchanges about dolls and humans occur as Togusa uncovers a model of the mansion, witnessing his and Batou's replayed movements within. This echoes again as they return to find the environment subtly altered, with the letterings "2501" emerging—signifying Batou's connection. The tension mounts as a battleship begins shelling the mansion, prompting reflections on his own identity and the essence of being human amidst technology. Batou realizes he has suffered a hack by a third party with ulterior motives.
With determination, Batou opts to assault the Locus Solus ship, embarking on a wild ride aboard a robo-whale underwater, while Togusa leverages his hacking skills to breach security. Batou infiltrates the ship, where robust defenses engage him, and he soon becomes surrounded by gynoids. In a surprising twist, one gynoid aligns with him, fighting back against the guards. During a moment of clarity, Batou recognizes Major Kusanagi using the gynoid as a remote avatar. Together, they fend off the onslaught of enemies while Kusanagi expertly hacks the ship's systems just as Batou exhausts his ammunition.
Kusanagi orchestrates their escape, redirecting the ship toward Japan waters to secure evidence against Locus Solus. Unlocking a room filled with machinery, they discover the gripping truth: Locus Solus has been illegally brainwashing girls supplied by the Kojinkai, transferring their consciousness into the gynoids. A faint cry of "help me" leads Batou to free a girl from the dubbing apparatus, realizing the connection to the earlier 3D photo. Before departing from the puppet body, Kusanagi reassuringly tells Batou that she will remain within the 'net, providing a sense of closure.
In a gentle denouement, Batou returns home, greeted by his cherished basset hound and observing the eerily lifelike doll placed by Togusa's daughter, a poignant reminder of the journey they have traversed.
