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The film begins at the conclusion of the The Girl Who Played with Fire. Salander is airlifted to a hospital in Gothenburg, to recover from gunshot wounds inflicted by her father, Zala. She is cared for by Dr. Anders Jonasson, who prevents anyone except Annika Giannini, her lawyer, from visiting.
At the same time, Evert Gullberg and Fredrik Clinton, old colleagues from the "Section," a group within the Swedish Security Service, reconnect and decide that they must silence Zalachenko and Salander to preserve cold-war secrets. Zalachenko is still alive, in a hospital room down the hall from Salander. Gullberg arrives at the hospital at the same time as Giannini, proceeds to Zalachenko's room, and shoots him dead. Giannini saves Salander by barricading the door to Salander's room. Gullberg, unable to reach Salander, shoots himself. Clinton visits psychiatrist Dr. Peter Teleborian, and explains his plan to silence Salander by having her committed to St. Stephen's mental hospital again. Dr. Teleborian tries to meet with Salander to conduct a psychological evaluation, but is obstructed by her doctor, Dr. Jonasson.
Blomkvist persuades Dr. Jonasson to sneak an internet phone (a Sony Ericsson Xperia X1 in the film) into Salander's room, whereupon Salander immediately contacts her fellow hacker, Plague, to see if he can find something on Dr. Teleborian. She then tells Blomkvist that Giannini has permission to use a video showing Nils Bjurman in the act of raping her. Bjurman was her state-appointed guardian and one of the people she is accused of murdering. Blomkvist compels a civil servant, Bertil Janeryd, to reveal that Gullberg and Rottinger had visited the Prime Minister years ago to urge a cover-up of the Zalachenko affair.
Salander starts working on an autobiography to document her actions and motives from childhood to the present. She continues to have nightmares of memories about her time at St. Stephen's, her father and half-brother, and of her two-hour ordeal with Bjurman. Blomkvist continues to pursue Dr. Teleborian with Christer's help. Salander finishes her autobiography and e-mails it to Blomkvist, and Dr. Jonasson informs Lisbeth she cannot remain at the hospital, but must be transferred to prison in a few days. He is surprised that she is not worried about the trial.
Niedermann, who previously tried to kill Salander's lover Miriam, has remained a fugitive, wanted for killing a police officer. Sonny, of the outlaw motorcycle gang from the previous film, is informed that he was searched, but found clean, and that his friend had sent Niedermann to hide out in his home. There, he finds his brother dead and his girlfriend tied, gagged, and apparently assaulted. She tells him that Niedermann was the culprit, and Sonny vows revenge. Clinton, in dialysis, is given a copy of Salander's autobiography, and is told that none of it can be proven. Meanwhile, Berger has been receiving anonymous e-mail threats, which causes an uproar in the office. In prison, Salander is interrogated by the prosecutor, but says nothing. Giannini is later given Salander's computer and the DVD of her sexual abuse. Niedermann breaks into an abandoned warehouse and kills a bicyclist who happens to be there having his lunch. Dr. Teleborian finally meets with Salander, who again remains silent.
When Berger's bedroom window is smashed, she calls Milton Security. Thanks to surveillance by Milton Security, Blomkvist learns that someone that night broke into his apartment and planted cocaine and cash there. He concludes that the Section are trying to frame him, since they cannot hurt the Millennium magazine itself. Blomkvist decides to meet Berger at a restaurant named "Samir's Gryta." The police try to warn Berger of an attempt to kill them there, and Blomkvist fends off the assault as the police rush to the restaurant. The Section becomes dismayed upon learning of the failed attempt.
On the day of her murder trial, Salander finally sheds her hospital-patient persona and enters court with piercings, a mohawk hairstyle, black makeup, and expensive black leather clothing. Called as an expert witness for the prosecution, Dr. Teleborian characterizes Salander's autobiography as merely the product of her paranoid delusions. Giannini gradually demolishes Dr. Teleborian's credibility, using Salander's words and files from the hospital. She shows 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. Called to the stand, Blomkvist shows that Dr. Teleborian had written his final psychiatric evaluation of Salander after being denied access by her doctor. Then Giannini calls Edklinth to the stand, and he states that the opinions were formulated in cooperation with Jonas Sandberg, using his computer as proof. Dr. Teleborian is left speechless. Edklinth tells Dr. Teleborian he is to be arrested on charges of possessing over 8,000 items of child pornography (which Plague had discovered after hacking into his laptop), and his computer is seized as evidence. After Dr. Teleborian is arrested, the court rules that no further need exists for Salander to be held in police custody.
The Millennium staff celebrate their victory, as Erika returns and reconciles with Mikael. Salander is encouraged by Giannini to check the property she has inherited from Zala and discovers the warehouse where Niedermann was hiding. Niedermann attempts to trap her there and kill her, but she is too fast and clever for that. She ambushes him with a nail gun and attaches Niedermann's feet to the wooden platform on which he is standing. His inability to feel pain finally works against him. By the time he realizes what is happening, it is too late for him to escape. She considers nailing him in the head, but instead phones Sonny and tells the bikers where to find him. Then she calls the police.
Salander returns home, and Blomkvist briefly visits to tell her that the motorcycle gang killed Niedermann and were arrested at the warehouse afterwards. Lisbeth and Mikael have a brief conversation that might or might not be a prelude to a further relationship.
Who is Salander's girlfriend?
Miriam