The film begins at the conclusion of The Girl Who Played with Fire. Computer hacker Lisbeth Salander is airlifted to a hospital in Gothenburg to recover from gunshot wounds inflicted by her father, crime boss Alexander Zalachenko. Journalist Mikael Blomkvist, who Salander helped on a previous case, resumes his efforts to clear her of several murder charges, knowing that she was framed by the "Section", a group within the Swedish Security Service that illegally sheltered Zalachenko after he defected from the Soviet Union.
Section members Evert Gullberg and Fredrik Clinton decide to silence Zalachenko and Salander to preserve their secrets. Gullberg arrives at the hospital and kills Zalachenko, but is unable to reach Salander; he then commits suicide. Clinton plans to have Salander recommitted to the mental hospital where the Section had her institutionalized as a child after she nearly killed Zalachenko. His collaborator in this plan is Dr. Peter Teleborian, the hospital's administrator, who "treated" the young Salander by putting her in restraints for the smallest infractions.
Blomkvist persuades her doctor to sneak an Internet phone into Salander's room, whereupon Salander contacts her fellow hacker, Plague, to see if he can find something on Teleborian. She then tells Blomkvist that Annika Giannini, her lawyer and Blomkvist's sister, has permission to use a video showing her state-appointed guardian Nils Bjurman raping her; Bjurman, a former Section employee, is one of the people she is accused of murdering.
Ronald Niedermann, Zalachenko's son and enforcer who previously tried to kill Salander's girlfriend Miriam, remains a fugitive, wanted for killing a police officer. Sonny, a member of an outlaw motorcycle gang Salander encountered in the previous film, learns that Niedermann went to his home to hide out. There, Sonny finds his brother dead and his girlfriend badly injured. She tells him that Niedermann was the culprit, and Sonny vows revenge.
On the day of her murder trial, Salander enters court with piercings, a mohawk, black makeup, and black leather clothing. Called as an expert witness for the prosecution, Teleborian characterizes Salander as delusional and violent; but Giannini gradually demolishes his credibility, using Salander's words and files from the hospital. She also presents the video proving Bjurman raped Salander.
As Giannini presents her case, the police arrest the people involved with the Section and seize their place of operation. In court, Blomkvist and Giannini prove that Teleborian made a false diagnosis on orders from the Section, and that the evidence against her was planted. Teleborian is then arrested for possession of child pornography, which Plague discovered after hacking into his laptop. The court releases Salander.
Salander checks on a property she has inherited from her father and discovers the warehouse where her step-brother Niedermann is hiding. He tries to kill her, but she nails his feet to the floor with a nail gun. She calls Sonny and tells the bikers where to find him, and then calls the police.
Blomkvist visits Salander to tell her that the motorcycle gang killed Niedermann and were arrested at the warehouse afterward. They then reconcile and go their separate ways.
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