On her return to Sweden after nearly a year away, Lisbeth Salander reconnects with her former partner, Miriam Wu, generously offering her the free use of her old apartment. However, things take a dark turn when Salander confronts her abusive ex-guardian, Nils Bjurman, after hacking into his email and discovering his appointment with a tattoo removal specialist. With a gun in hand, she warns him to leave the tattoo she marked on him—labeling him a rapist—untouched.
Simultaneously, journalist Mikael Blomkvist enlists the help of fellow reporter Dag Svensson to assist with an article for his magazine, Millennium. Dag's exposé focuses on prostitution and human trafficking within Sweden, while his girlfriend Mia Bergman researches sex trafficking for her doctoral thesis. Planning a holiday, they ask Blomkvist to collect some photographs from their apartment, and Dag also requests him to look into a name—“Zala”—that may be connected to the subjects of their work.
Upon arriving at their apartment, Blomkvist is met with horror as he discovers the lifeless bodies of Dag and Mia. The investigation reveals that the handgun used in the double murder belongs to Bjurman, who has also been found dead. With Salander becoming the prime suspect due to her fingerprints on the weapon, she initially refuses to claim innocence but eventually confesses to Blomkvist that she had no part in the murders and emphasizes the necessity of uncovering the identity of “Zala”.
Paolo Roberto, Salander's boxing trainer, reaches out to Blomkvist, offering a potential lead by connecting with Miriam. He witnesses Miriam’s abduction by Ronald Niedermann, a dangerous figure involved in human trafficking. Paolo follows Niedermann to an isolated barn, where he hears him torturing Miriam for information about Salander. Attempting a rescue, Paolo is overpowered, yet both he and Miriam manage to escape as the barn goes up in flames.
The attempt is reported in the news, prompting Paolo to give his testimony to the police. In the meantime, Blomkvist leaves vital information on his computer for Salander to access, leading to a heartfelt message where she thanks him for his friendship. Realizing the peril she faces, he understands she plans to confront the individual responsible for framing her, potentially putting her life at risk.
In a twist of fate, Salander visits Miriam in the hospital, offering an apology for entangling her in this dangerous scenario. After confirming the police sketch of Niedermann, she vanishes. Miriam contacts Blomkvist with a set of keys Salander dropped, one of which leads him to her post office box, allowing him access to crucial information about her whereabouts. Meanwhile, Salander keeps a close watch on Niedermann's post office box, eventually trailing him to a secluded house near Gosseberga. Blomkvist, in Salander's apartment, uncovers a harrowing video of Bjurman's assault on her.
Paolo later meets with Blomkvist, revealing that he tracked Niedermann down and learned about his rare condition—congenital analgesia—which prevents him from feeling pain. Their investigation points to a company linked to “Karl Axel Bodin.” With urgency, Blomkvist has his colleague and lover Erika Berger forward documents regarding their findings to the police and embarks on a mission to find Salander.
As Salander confronts Niedermann in the Gosseberga house, he is alerted and ambushes her, knocking her out cold. Upon waking, she faces her father, Alexander "Zala" Zalachenko, who she hasn’t seen since her childhood when she set him on fire. Their tense interaction unveils that Niedermann is her half-brother, and he murdered Bjurman to keep Zalachenko's secrets buried.
In a climactic twist, they lead Salander to a shallow grave in the woods. Defiantly, she declares that the police will soon find him as she reveals his secrets have already made their way online through her hidden cellphone. Skeptical, Zalachenko shoots her multiple times as she attempts to flee and buries her alive. Refusing to succumb, Salander digs her way out, retaliating by burying an axe in Zalachenko's leg. As she holds Niedermann at bay with Zalachenko’s gun, Blomkvist arrives just in time. An ambulance comes to rescue both Salander and Zalachenko, but not without leaving them both severely injured.
