In a futuristic world where the majority of humankind has been enhanced with cybernetic augmentations, Hanka Robotics stands as the leading authority in augmented technology. They embark on a highly secretive project to create a mechanical body, or "shell," capable of housing a human brain instead of relying on AI. This groundbreaking initiative brings Mira Killian (Scarlett Johansson), a young woman and the sole survivor of a devastating cyber-terrorist attack that claimed her parents' lives, into the fold. After her physical body is severely compromised, she is selected as the initial test subject for this experimental procedure. Though her designer, Dr. Ouelet (Juliette Binoche), voices strong objections, Hanka's CEO, Cutter decides to repurpose Killian as a counter-terrorism agent.
Fast forward a year, and Mira has risen to the rank of Major within Section 9, the anti-terrorist division. Alongside her teammates, Batou (Pilou Asbæk) and Togusa (Chin Han), under the command of Chief Daisuke Aramaki (Takeshi Kitano), she successfully thwarts a terrorist plot aimed at a Hanka business conference. This culminates in an intense showdown where Killian destroys a rogue mechanical geisha, who has taken a hostage's life.
However, as Killian grapples with hallucinations that Dr. Ouelet dismisses as mere "glitches," she's increasingly haunted by fragmented memories of her past. When she discovers that the mechanical geisha was compromised by an enigmatic hacker named Kuze (Michael Pitt), she deviates from protocol and delves into the AI's workings to seek answers. The situation escalates as Kuze attempts a counter-hack, prompting Batou to sever her connection.
With the information at hand, they track the hacker to a Yakuza nightclub, where they fall into a dangerous trap, leading to a catastrophic explosion that injures Batou and severely damages Killian's body. Enraged by her insubordination, Cutter threatens to dissolve Section 9 unless Aramaki maintains control over her actions.
As tensions rise, Kuze, intent on vengeance, targets Section 9's Hanka advisor, Dr. Dahlin (Anamaria Marinca), ultimately killing her. This prompts the team to connect her death to the murders of other senior Hanka researchers, leading them to suspect that Dr. Ouelet could be next. In a race against time, Batou, now equipped with cybernetic vision after losing his eyes in the nightclub explosion, manages to kill one of the assassins while Killian confronts the other. During interrogation, Kuze momentarily controls the surviving assailant before forcing him to take his own life.
Togusa, following the digital trail, discovers a clandestine location housing numerous individuals mentally interconnected within a signal network. Killed in the ensuing chaos, Killian finds herself in confrontation with Kuze, who reveals his identity as another failed Hanka test subject, urging her to question the authenticity of her memories. He ultimately frees her but escapes before Killian can further engage.
Revisiting Ouelet, she learns shocking truths: there were 98 test subjects before her, and her memories have been artificially implanted. Fearing Killian's potential threat, Cutter orders her termination upon her return. In an act of rebellion, Ouelet presents Killian with a crucial address to escape to safety. Though Cutter tracks them down and murders Ouelet, he falsely shifts the blame onto Killian, declaring her a rogue element.
Killian uncovers the address to an apartment belonging to a grieving mother, who tells her about her daughter, Motoko Kusanagi (Scarlett Johansson), who had gone missing about a year ago. Struggling to process this revelation, Killian reaches out to Aramaki while trying to connect the past pieces of her life. Aramaki cunningly allows Cutter to overhear their communication, setting off a series of interventions where Batou, Togusa, and Aramaki take out Cutter's ambush.
Following the trail of her memories leads Killian to Motoko's last hiding place where she reconnects with Kuze. They share vivid recollections of their past as anti-augmentation activists abducted by Hanka. Just as they begin piecing everything together, Cutter sends a "spider-tank" to eliminate them. Though Kuze suffers a near-fatal injury, Killian manages to disable the tank but sacrifices her left arm in the process. Mortally injured, Kuze proposes merging their "ghosts," but before they can bond, a Hanka sniper extinguishes his life.
After being rescued by Batou and the team, with Aramaki taking justice into his own hands by executing Cutter, Killian awakens to a new dawn. Rebuilt and embracing her true identity as Motoko, she reconciles with her mother and resumes her duties with Section 9, now fully aware of who she truly is.
