A police bulletin reports a 208 is in progress in the C13 area of New Port City. A figure studies a night-scope green image of men talking about programming bugs and Project 2501. A voice reports Section 6 is ready to move in. Major Motoko Kusanagi disconnects wires from the back of her neck and stands up, takes off her overcoat. She does a back layout fall from the top of a tall building. A group of armed and helmeted police enter a building. Inside a room four men are surprised that the police have arrived and two draw their weapons and go to the door to start firing. The older man of the group tells the others to stop shooting and as the police storm the room he claims diplomatic immunity.Nakamura, the head of Section 6 enters to say that taking a programmer out of the country is an offense. However, the young programmer has signed a request for asylum. Suddenly a voice speaks out and assaults the foreigner, an invisible attacker rips the man apart. The police fire at the windows, Nakamura goes to a smashed window to see Major Kusanagi falling and becoming invisible as her thermoptic camoflage turns on again.Title sequence begins showing a cyborg female body undergoing a genesis. Major Kusanagi ascends from a pool of liquid. She awakens from sleep in a dark room, looks pensively out the window then gets dressed in a combat suit and leaves her apartment.A VTOL twin-rotor craft lands on the roof of a tall building. The Japanese Foreign Minister leaves the aircraft and begins talking to the waiting Aramaki, the head of Section 9. They discuss a secret meeting with the Gavel Republic planned for the next day. Gavel has a new revolutionary government and the leader of the old ruling junta is seeking asylum in Japan. The Foreign Minister admits he'd like to deport Col. Maless if he had a good political excuse. He also thanks Section 9 for helping with the programmer defection, as this way the diplomatic corps was able to keep their hands clean.In a lab a group of red-suited techs and Major Kusanagi are studying an unconscious woman, trying to access her brain. She is the Foreign Minister's Interpreter, and has been cyber-brain hacked since 23 minutes earlier while on the phone. Aramaki suggests someone called the Puppetmaster is trying to disrupt the talks with Gavel by turning her into an assassin. Batou and Ishikawa are in a car tracing the signal, the Major goes to rendezvous with them.In their van, the Major dresses in armour as Togusa drives, they discuss the Puppetmaster. He is believed to be an American but nothing else is known about him. He has been active around the world conducting cyber terrorism and ghost-hacking people's brains. This is the first time he has appeared in Japan. They consider it may all be disinformation, then the Major chides Togusa for still using an old style handgun, as she loads and locks a large automatic rifle. Togusa is curious on why he was recruited into Section 9, the Major replies it is because he is still mainly human and so can be an unpredictable non-specialized asset on the team.On an inner city street two garbage collectors are at work. One urges the other to hurry up as the partner is busy at a public access computer terminal. The computer user explains a guy in a bar gave him some software so he could ghost hack his estranged wife. As they drive off Batou and Ishikawa arrive in a hurry and realize they just missed their target, yet again. They talk to a local and begin to suspect the garbagemen. Kusanagi plugs into the net and with Section 9 HQ quickly determines the trash route coincides with hacking locations. She takes over driving the van and issues orders to Batou and Ishikawa. The garbagemen are alerted the police are investigating and the hacker husband decides to go to his programmer friend. Togusa and the Major get close. The vehicles arrive together near a man wearing sunglasses at another 'net station. He fires a submachine gun and takes out the Section 9 van. The Major and Togusa scramble out of the wreck as the shooter continues to riddle the van with armour piercing shells. Batou arrives on the scene and the shooter cloaks himself with thermoptic camoflage and tries to escape.Batou notices the blurry camo and fires back. The Major goes to the rooftops to scan. The man enters a crowded street market area. A wild gunfight continues as Batou gives chase. The Major tries also but the man seems to escape and stands in a shallow waterfront. An invisible Major Kusanagi proceeds to kick the man senseless. On questioning Batou and the Major realize the man was also a hacked puppet.Outside a large estate house Aramaki and Section 9 prepare to assault. A helicopter lands on the lawn and a man they believe to be the Puppetmaster disembarks. Further questioning of the garbageman reveals he has been hacked also and given false family memories.Major Kusanagi floats from the depths of the harbour. Batou greets her onboard a boat and asks why she dives. They drink beer and reflect on being high maintenance supercyborgs. The Major speaks briefly in a different voice.In a grimy cityscape the Major rides a water ferry and gazes at the city around her. A sad eyed beagle stares back.On a roadway at night a blonde woman is hit by a car. In the Section 9 lab she is a cyborg wired up and is electro-shocked. She had been built two hours earlier at Megatech and escaped. The body has no organic brain but does have semblance of a ghost. The Major decides to dive into the brain to investigate and pauses to reflect on her own existence.Nakamura from Section 6 Treaties Section of the MFA arrives with an associate. Nakamura shows a card signed by the Foreign Minister and demands the cyborg body. In the parking garage Togusa is suspicious and checks the video of the Section 6 arrival. He reports the men may have come in with thermoptic camoflaged cyborgs.In the lab Aramaki and Nakamura view the partially dissembled torso of the mystery cyborg. The other Section 6 man, Dr. Willis, starts keyboarding and confirms the the cyborg is the Puppetmaster. Section 6 has also been chasing him and they lured him into the cyborg body. The torso comes alive and states it's name is Project 2501, a self aware computer program and requests political asylum.The camoflaged Section 6 cyborgs attack and grab the torso. Before driving away Togusa manages to hit the car with a tracking device bullet. Aramaki authorizes Section 9 to retake Project 2501, but to destroy it if they can't recover it. Meanwhile Ishikawa reports on his investigation. Dr. Willis and the defecting programmer from earlier developed Project 2501 for Japanese Foreign Ministry diplomatic dirty tricks, but somehow they lost control of it. Section 6 is trying to cover it all up.Out in the city Batou realizes there is a decoy car, The cars split up. The one Batou is chasing hits a roadblock and the two men inside are killed by sniper fire. Kusanagi in a helicopter overlooks the other car. She rappels down with her warbag then realizes the car is protected by a large cloaked walking tank. The Major loads up with heavy ammo as Batou rushes to help. After a hot and heavy firefight The Major gets on top of the tank and tries to lift the hatch. Her arms tear off and the tank grappels her head and shakes her like a doll. Batou arrives with an anti-tank weapon and takes out the armoured vehicle. He takes the Project 2501 torso from the car and places it beside the wounded Motoko. In the skies above two Section 6 helos observe and prepare. Batou wires up the Major to the torso.Project 2501 speaks through the Major and explains himself. He states he learned of Section 9 on the 'net and planned this joining up. Project 2501 wants to experience real life and death and proposes a merger with the Major. Batou is unable to disconnect the wires as the Section 6 targeting lasers rove over the female bodies. Section 6 is hacked to give the merger more time. As the Major sees the light the blond torso is destroyed with a headshot. Batou manages to partially cover the Major's face with his arm as another Section 6 shot seems to destroy Kusanagi.In an apartment a young girl with blank eyes sits in a armchair. The girl stirs and is greeted by Batou, it is Kusanagi in the only body Batou could find. 20 hours have passed since the shooting, the Foreign Minister has resigned but the incident will be covered up. The girl gets up to leave and tells Batou she is neither the Puppetmaster nor Major Kusanagi, rather a new being. The newborn states "the 'net is vast and infinite" as she leaves the safe house.