Plot

In the year 2032, Batô, a cyborg detective for the anti-terrorist unit Public Security Section 9, investigates the case of a female robot--one created solely for sexual pleasure--who slaughtered her owner.

Batô is a living cyborg. His whole body, even his arms and legs, are entirely man-made. What only remains are traces of his brain and the memories of a woman. In an era when the boundary between humans and machines has become infinitely vague, Humans have forgotten that they are humans. This is the debauchery of the lonesome ghost of a man, who nevertheless seeks to retain humanity. Innocence... Is what life is.—Anonymous

An insectoid single seat helicopter flies over a high rise city at night. Down below Batou drives his car through a pedestrian filled street and arrives at a crime scene. The cops tell him a perp killed two cops. Batou cocks his shotgun and goes into a dark alley by himself. He finds the dead police and also a female figure sitting quietly. She attacks Batou, but he punches her out easily. She whispers "Help me" and reveals herself to be a cyborg.

Title sequence showing a stylized birth/genesis of a cyborg form.

Section 9 view a briefing describing eight recent killings by the Locus Solus #2052 "Hadaly" type gynoids, which then self-destruct. Aramaki explains Section 9 is now involved because there have been no civil lawsuits, a politician and a retired public servant are among the victims and terrorism is a possibility. He tells Batou and Togusa to check out the gynoids while Ishikawa and Azuma check background.

In the car Togusa and Batou discuss the missing Major Kusanagi. They drive to the police Forensics lab. They meet a chain-smoking weary cyborg technician, Miss Haraway, who has been examining the alley-way gynoid Batou captured. The gynoids are somehow able to free themselves of moral code #3, not to harm humans. She theorizes on why robots commit suicide. Haraway also explains the gynoids are "sexaroids" equipped with otherwise unnecessary organs. Togusa understands why the victim's families have settled out of court. The alley-gynoid brain was wiped clean except for the audio phrase "help me".

Back in the car the two S9 agents plan to find the manufacturer's inspector when the Section 9 dispatcher reports a "602", the victim is the Locus Solus inspector at a boathouse. On scene they find Ishikawa already there. The dead man is Jack Volkerson, age 54 who has been missing for five days. The kitchen sink and bathroom are splattered with blood and bloody knives. Batou finds a 3D photo of a young girl. The three men leave as a Forensics CSI team arrive.

Ishikawa drives Batou home, they stop to buy some dog food, Ishikawa suggests dry food is better. Batou gets out of the car and misdirects Ishikawa on where his apartment is. Entering his flat Batou is greeted by a playful large basset hound. Batou carefully cooks a meal for the dog and quietly relaxes with a beer.

Section 9 view a forensics report on Volkerson, it indicates he was killed with a hit to the neck and then dismembered and eviscerated. A deformed door knob at the scene suggests someone with an illegal cyber hand "claw" was there. Also, a car registered to a local yakuza group "Kojinkai" was found nearby. It turns out a gynoid killed the head of the Kojinkai group three days ago. It may be a revenge killing but Aramaki tells Togusa and Batou to continue, the rest go back to regular duties. In a private moment, Aramaki cryptically asks Togusa to keep an eye on Batou's emotional state.

In the garage Batou loads heavy weapons into the trunk, Togusa is alarmed and only wants to talk to the yakuza. Arriving at the Kojinkai club with several men lounging about, they demand to see Wakabayashi, the new leader. The gangsters draw weapons but Batou is quicker and starts cutting them down with his own automatic rifle. More yakuza arrive and a wild firefight continues, Batou takes them all out. The two agents explore upstairs and find the leader and the mutant claw cyborg. Batou makes short work of the cyborg, a terrified Wakabayashi claims Locus Solus told them where Volkerson was but he doesn't know what the former leader was doing with the robot company. Later, Aramaki mildly reprimands Batou and Togusa for acting like vigilantes.

Togusa drops Batou off at his favourite mini-mart. A short figure warns him of a kill zone and Batou warily scans the other shoppers. A gunfight erupts and Batou is hit several times, his cyber vision starts to fail. Suddenly ishikawa appears with a pistol grip plugged into the back of Batou's neck. Back in the Section 9 lab Batou awakens with a new arm. He had been brain hacked and made to shoot himself. Ishikawa and Togusa arrive with the pet basset. Batou always went to that store because it was the only place that had the special dog food. Batou and Togusa decide to go after Locus Solus in the Northern Frontier.

They fly to a strange industrial looking city, tall towers that resemble oil refinery cracking towers and radio antennae. A former special economic zone it is now a crumbling lawless place. The bird-like VTOL craft lands at an old medieval-style cathedral. An elaborate and colourful parade makes it's way down a canal. Batou and Togusa find an old snitch, Lin, and ask him about a man named Kim. Outside a large mansion Batou explains that Kim is a former military electronics expert. They enter the house and into a luxurious foyer. A female doll-like figure has the letters "aemaeth" displayed before it. The two S9 men go upstairs to a library. They find a dessicated corpse-like cyborg. Batou realizes the body is a sham and tells Kim to talk, they know each other from the war years earlier. Kim explains that Locus Solus is making the gynoids on a factory ship in international waters. Kim talks rhetorically about dolls and humans. Togusa finds a model of the mansion and looks into a window. He sees himself and Batou as they walk toward the mansion as a replay. Once again they enter as before, the foyer is slightly different, this time the doll has the letters "maeth". Kim's body upstairs is now a replica of Togusa. Kim continues to philosophize on men, machines and computers. Suddenly another replay of the two entering the mansion. In the foyer the doll is gone and the letters on the floor are "2501". Now the Kim body is a Batou replica. Offshore a battleship starts to shell the mansion, in the wreckage Togusa sees himself as a cyborg. Back to reality, Batou tells Togusa he has been hacked. He also explains the "maeth" message is from his "guardian angel" warning them. While Kim is a dead end, Batou decides to attack the Locus Solus ship, he rides a robo-whale underwater as Togusa clears security by hacking the system from an escort vessel using what is left of KIm's ebrain.

Batou enters the ship. The security system realizes there is an intruder and makes attempts to stop Batou. Togusa and Kim are zapped by a bolt of energy. On the ship the robo-guards go after Batou. One of the gynoids comes to life and starts fighting the guards. Other gynoids attack Batou, he is surrounded. One gynoid descends to fight alongside Batou, after a lull they talk and Batou realizes it is Major Kusanagi, using the body as a remote puppet. The two continue to mow down the attacking gynoids. Kusanagi opens a data terminal and plugs in to hack the shipboard system. She is able to shut it all down just as Batou empties his last ammo clip.

Kusanagi directs the ship to move south to Japan waters, it will be evidence against Locus Solus. Exploring further they enter a room where there are large devices. Locus Solus was illegally brainwashing girls supplied by the Kojinkai mob and dubbing the ghosts into the gynoids. Batou hears a faint "help me" and rescues a young girl from the dubbing apparatus, she is the same as from the 3D photo at the ea;l. They realize Volkerson had changed the ethics codes so that when the gynoids made trouble someone would notice and eventually come to save the girls. Kusanagi departs the puppet body after telling Batou she'll always be in the 'net.

At Togusa's house Batou gets his pet back and notices the daughter's life-like doll.