A severely wounded Lisbeth Salander is placed in intensive care at Sahlgrenska Hospital. It picks up where The Girl Who Played with Fire left off, two rooms away from her also-injured father, Alexander Zalachenko, whom Salander injured with an axe. Ronald Niedermann, Zalachenko's son and Salander's half-brother, steals 800,000 kronor from his outlaw motorcycle gang before disappearing. These events prompt immediate action from "the Section", a secret counterintelligence division of Säpo which shielded the abusive Zalachenko and forcibly institutionalized Salander after she attempted to kill him as a child. Evert Gullberg, founder and former chief of the Section, plots to deflect attention by silencing Salander, Zalachenko, and Mikael Blomkvist, the publisher of Millennium magazine. Meanwhile, Dr. Peter Teleborian, the corrupt psychiatrist who abused Salander during her institutionalization, provides prosecutor Richard Ekström with a false psychiatric examination so that she can be recommitted.
Gullberg, who has terminal cancer, shoots Zalachenko in his hospital bed. He attempts to enter Salander's room to kill her as well, but is thwarted by her lawyer, Annika Giannini, leading to him committing suicide. Section operatives also murder Gunnar Björk, Zalachenko's former Säpo handler and Blomkvist's source of information for an upcoming exposé; the operatives falsify the death as a suicide. Other operatives break into Blomkvist's apartment and mug Giannini, making off with copies of the classified Säpo file that contains Zalachenko's identity and planting bugs in the homes and phones of Millennium staff. The timing of the attacks and the property that was taken cause Blomkvist to realise that the phones are tapped, and he begins to investigate the Section in earnest.
Blomkvist hires Dragan Armansky's Milton Security to handle countersurveillance. Armansky, on his own initiative, informs Säpo official Torsten Edklinth about the violations of Salander's constitutional rights. Edklinth, along with his assistant Monica Figuerola, begins a clandestine investigation into the Section. After Figuerola confirms the allegations, Edklinth contacts the Justice Minister and the Prime Minister, who approve a full investigation and later invite Blomkvist to a confidential meeting in which they are to share information. They agree to Blomkvist's deadline—he intends to publish his findings about the Section's actions on 15 July, the third day of Salander's trial, and the government agree to arrest any identified ringleaders of the Section at the same time.
Blomkvist arranges to have Salander's handheld computer returned to her, and has a cellular phone placed in a duct near her room to give her an online hotspot through which to maintain contact with the outside world. Meanwhile, Blomkvist, Armansky, and their allies continue their joint counter-surveillance of the "Zalachenko club", feeding them misinformation about Millennium's (supposed) passivity regarding Salander's trial, identifying nine central players in the Section. The Section catch on to the ruse and arrange to plant cocaine in Blomkvist's apartment and hire two members of the Yugoslav mafia to murder him; their intention is to frame him as a drug dealer and thus destroy his credibility. The dual plot is foiled, and Blomkvist and Berger are spirited off to a safehouse.
On the third day of Salander's trial, Millennium's exposé causes a media frenzy and officers of the Section are arrested. Giannini systematically destroys Teleborian's testimony, proving that he and the Section conspired to commit Salander to protect Zalachenko and that his recent "psychiatric assessment" of her was fabricated. The most powerful testimony on Salander's behalf is the playing in court of the secret video recording Salander made of her rape by her former guardian, which Teleborian had dismissed as a schizophrenic fantasy. Teleborian is then arrested for possession of child pornography. Ekström, realising that the law is on Salander's side, withdraws all charges against her, and her declaration of incompetence is rescinded.
Freed, Salander spends several months at Gibraltar. She soon discovers that, as Zalachenko's daughter, she is obliged to inherit half of his properties and wealth, while the other half goes to her twin sister Camilla, whom no one has heard from in more than a decade. Suspicious about an abandoned factory in her father's estate, she goes there to investigate. There, she discovers Niedermann, who had been hiding there from the police. After a brief struggle and chase, Salander outwits Niedermann by nailing his feet to the plank floor with a nail gun. She is tempted to kill him herself, but instead reports his location to the biker gang, and then reports the entire brawl to the police. Back at her apartment in Stockholm, Salander receives a visit from Blomkvist. The story ends with the two reconciling as friends.
