In the near future, humans have become enhanced with cybernetic upgrades. Hanka Robotics Corporation is the top company in this type of technology, and is on the verge of developing a new kind of cyborg that uses a human brain to function. A woman, named Mira Killian (Scarlett Johansson), is being taken into Hanka after an accident. Her brain is placed into the body of a cyborg with greater strength and agility. Once the process is complete, her designer, Dr. Ouelet (Juliette Binoche), speaks to Hanka's CEO Cutter (Peter Ferdinando). Cutter wants to place Mira in Section 9, an anti-terrorism squad, but Ouelet feels she is not ready for something like that.
One year later, Mira is now known as The Major. She is on the roof of a building listening in on a meeting between Hanka representative Dr. Osmond and an African Ambassador (Chris Obi). The Major receives her orders from Section 9 Chief Daisuke Aramaki (Takeshi Kitano) and works alongside Batou (Pilou Absaek) and Ladriya (Danusia Samal). In the conference, several geisha-bots start to attack the people in the room, leading The Major to spring into action, against Aramaki's orders. She goes invisible and jumps off the roof before swinging into the room and she starts shooting the geisha-bots. One of the geisha-bots hacks into Dr. Osmond's neck and kills him before The Major gets to it. The geisha-bot says "Commit to the will of Hanka and be destroyed." The Major shoots it.
The Section 9 team meets with Aramaki to discuss the attack. They learn that the geisha-bots were hacked from a mysterious source, also uttering the same phrase that the geisha-bot said to The Major. The rest of the team leaves but Aramaki talks to The Major about her move by jumping into the room. Aramaki informs her that she still has her ghost (her soul) within her shell (her cyborg body). The Major meets with Dr. Ouelet frequently to repair her body when it has been damaged. The Major has trouble remembering her past, only seeing brief glimpses and flashes. Ouelet dismisses her hallucinations as glitches, but she is shown to care for The Major.
The Major and Batou are driving around the city. She mentions what little memory she has of her past, which involves her family dying getting to the country. On the road, The Major sees a hallucination of a burning hut. The Major and Batou meet with Dr. Dahlin (Anamaria Marinca) with the geisha-bot body. The Major deep-dives into the geisha-bot's AI to try and get more answers on the hacker. The Major finds herself walking through a club with distorted images. She is grabbed by the entity, forcing Batou to pull her out of the connection. The Major says she knows where to find the hacker.
The Major and Batou go to a Yakuza nightclub with Ladriya. The Major is pulled into a room by two men who force her to dance while she is handcuffed to a pole and is zapped by a cattle prod. The room also blocks a signal for her to communicate with Batou. The Major then starts fighting the men in the room, kicking one out of the room and leading to a shootout that Batou engages in. He and The Major kill a number of goons before they head off to find the hacker. They run toward a room that is really a trap. A bomb goes off that damages The Major's body and blinds Batou.
Batou receives cybernetic eyes to replace his damaged ones while The Major's body is repaired. Meanwhile, Cutter meets with Aramaki with anger over The Major doing the deep-dive. Aramaki warns Cutter who he is threatening since Aramaki answers to the Prime Minister and not Hanka. The hacker (Michael Pitt) finds Dr. Dahlin and rips her eyes out before killing her. The Section 9 team finds her body, and The Major pulls a drive out of Dahlin's hand which contains names of other Hanka associates, including Ouelet. They figure she is the hacker's next target.
The hacker controls two sanitation workers to ram their truck into Ouelet's car. She survives but the men step outside and try to shoot her. The Major and her partners arrive in time to shoot back at the men. She chases after one man, Lee, as he runs by a body of water. The Major fights him while invisible until Batou shows up and stops her. Lee is interrogated after the hacker's connection is severed. He informs Section 9 that he was on his way to pick up his daughter. The Major shows him a photo of what he sees as his daughter, but is really a picture of himself. They determine that the hacker placed fake memories in Lee's head. The hacker, whose name is learned to be Kuze, then speaks through Lee to threaten Section 9 before making Lee jump to hang himself with the cable around his neck.
Section 9 member Togusa (Chin Han) traces the hacker's signal to a hidden location. The Major finds Kuze as he is connected to a network with other humanoid cyborg bodies. Kuze reveals that he was a test subject of Hanka's, but considered a failure and a freak on account of his deformed outcome. The Major sees a tattoo on his chest of the burning hut like in her hallucination. Kuze says that Hanka took control over their lives instead of saving them.
The Major confronts Ouelet over the revelation. Ouelet says that there were 98 failed experiments before The Major became the first successful one. The Major appears angry even as Ouelet tries to defend her position. Cutter orders Ouelet to terminate The Major on account of her being a liability. As The Major undergoes the process, Ouelet instead gives her an address so she can find answers for herself. Ouelet allows The Major to escape, so Cutter shoots and kills Ouelet in revenge. Cutter reports to Aramaki that The Major killed Ouelet and that she must be terminated.
The Major follows the address to what turns out to be her old home. Her mother (Kaori Momoi) is there, having believed that her daughter ran away and was killed. The Major's real name was Motoko Kusanagi. Her mother does sense a familiar look in The Major's eyes when she looks at her. As she leaves, The Major gets in contact with Aramaki, who informs her that Ouelet is dead and that Cutter says she killed her, though they both know the truth. They allow Cutter to listen in on their conversation as they plan their next move. Cutter sends his men to kill Section 9 members, but Batou, Togusa and Aramaki all survive and kill their attackers. The Major meets with Kuze at a hideout, which resembles the burning hut. They learn that Kuze's real name was Hideo, and they were originally against augmentations with humans and cyborgs.
Cutter sends a spider tank to kill The Major and Kuze. However, the spider tank hits Kuze and severely damages him. The Major leaps onto the back of the spider tank and tries to rip its back open. She uses all her strength, causing her arm to rip off as she destroys the spider tank. One of Cutter's snipers rides in on a chopper and kills Kuze. Aramaki sends his own man, Saito (Yutaka Izumihara), to take down the sniper to save The Major. Batou recovers The Major, who is still alive. Aramaki then corners Cutter after having spoken to the Prime Minister. Aramaki contacts The Major and gets her consent to execute Cutter. He shoots Cutter three times as he falls into his own pool.
The Major visits her own grave with her mother, who now knows her daughter is still with her. The Major's voiceover states that she knows there will be more like her, but she knows her enhancements do not define her. She then returns to work with Section 9 and leaps off a building to her next mission.