Picking up immediately after the events in the previous movie 'The Girl Who Played With Fire', Lisbeth Salander (Noomi Rapace) is airlifted to a hospital in Gothenburg. Surgeons remove the bullets from her shoulder, hip, and head, where her father, Alexander Zalachenko, shot her. In the hospital, she meets Dr. Jonasson (Aksel Morisse), who cares for her throughout her stay, preventing anyone except her lawyer from visiting.
Niederman (Micke Spreitz) is now a fugitive, wanted for killing two police officers after escaping in the previous movie.
In Stockholm, a man named Evert Gullberg (Hans Alfredson) meets with his former colleague of 35 years, Fredrik Clinton (Lennart Hjulström); the two decide that they must silence Zalachenko and Lisbeth.
Zalachenko (Georgi Staykov) is still alive, in a hospital room down the hall from Lisbeth. He is met by a member of the "Section", a group within the Secret Police (abbreviated as Säpo), to decide how to conceal his existence. Zalachenko puts all the blame on Niederman, and threatens that if he were to be convicted, he would spill everything to the police and media.
Mikael Blomkvist (Michael Nyqvist) asks his sister, Annika (Annika Hallin), to be Lisbeth's lawyer, as she is accused of attempted murder as well as the three murders of Nils Bjurman, and Dag and Mia in the previous movie that she was never cleared of.
Gullberg arrives at the hospital at the same time as Annika, passing right by her. He then tells Zalachenko that they will not help him, before shooting him in the head. Annika saves Lisbeth by barricading the door to Lisbeth's room, preventing Evert from killing her too, and he shoots himself. Afterward, police are soon put outside Lisbeth's room, and Fredrik visits the Section headquarters to confirm that Evert shot Zalachenko, stating that he had chosen to do a final job because he was dying of liver cancer.
Fredrik visits Dr. Peter Teleborian (Anders Ahlbom), and explains his plan to punish her for trying to kill Zalachenko by having her committed to St. Stephen's mental hospital again. Teleborian tries to meet with Lisbeth to conduct a psychological evaluation, but Dr. Jonasson denies him entry and insists he make the necessary official requests.
Mikael and Annika lose both copies of the Björck investigation files, files needed to prove that Lisbeth was in fact being punished by corrupt men of law, as they were stolen under orders from Fredrik. Mikael then calls Milton Security in desperation.
Meanwhile, a representative from the Section speaks to the goverment prosecutor, Ekström, stating that if Zalachenko's secrets were to come out during Lisbeth's murder trial, relations with foreign countries and Säpo's secret contacts would be ruined, and that there are many useful background facts about the case, including her previously attempted patricide, that would help convict her.
The Millennium team work to find out more about the Section, but find it difficult since many of the politicians and Säpo workers would have leaked information about it in their autobiographies. Mikael then decides to uncover more information on Gullberg to find out more about the Section.
Mikael tells Dr. Jonasson the conspiracy against Lisbeth. He finds it unlikely, but Mikael assures Jonasson that it is true. Mikael then convinces him to sneak in her internet phone into the hospital. Upon receiving her phone, Lisbeth immediately contacts her hacker friend Plague to see if he can find information on Teleborian, and then tells Mikael that Annika has permission to use a video of Nils Bjurman her former guardian and one of the people she is accused of murdering raping her.
At the office the next day, Christer finds out that Gullberg and a man named Hans von Rotting visited the Prime Minister in 1976. Mikael decides to visit one of the secretaries, Bang Janeryd, and shows him the files. He says he had no idea what Zalachenko was doing, and that he wants nothing to do with the trial. Mikael forces him to either have his involvement revealed or tell Mikael what he knows and become a confidential source. He confirms that Gullberg and Rotting had visited the Prime Minister, as well as Fredrik Clinton. He tells Mikael that Zalachenko had cooperated with them and gave them invaluable information, and that everything was to be top secret at the time.
Plague contacts Lisbeth, and tells her that he did not find anything on Teleborian's work computer. She then suggests that he hack into his personal computer. He will do it, regardless of the difficulty. Later, a woman named Monica Figuerola of the police asks Mikael to meet with her and her boss Torsten Edklinth. They say that there is in fact an underground crime group that is involved with the government, and that Torsten's meeting with the Prime Minister resulted in a full investigation. They also inform Mikael that they need time to identify those involved, and that he must print the magazine after the investigation is over, because if not, it will be put in jeopardy. They are also aware of the torture Lisbeth was subjected to. Mikael then gives them a few of the names of those involved.
While still in the hospital, Lisbeth starts working on an autobiography to tell her life story to Mikael. She continues to have nightmares of memories about her time at St. Stephen's, her father and half-brother, and of her rape by Bjurman. When she wakes up, Niederman is outside of her window, and aims at her with a gun, but she moves out of his view before he shoots.
Mikael continues his story, and then follows Teleborian, with Christer's help. They also follow the Section member he is meeting with, which leads to a flat that Fredrik Clinton had been to four hours before. Lisbeth finishes her autobiography and sends it to Mikael, and Jonasson informs Lisbeth she can stay no longer and she will be taken away in a couple of days. Dr. Jonasson is surprised that she is not worried about the trial. Mikael finishes his story as well.
Another day or two later, Lisbeth is transfered out of the hospital and to a prison in Stockholm to await her murder trial.
Sonny, the motorcycle gang member from the previous film, is informed that he was searched by the police, but found clean, and that his friend had sent Niederman to hide out in his home. There, he finds his brother dead and his girlfriend tied, gagged, and apparently assaulted. She tells him that Niederman was the culprit, and Sonny vows revenge.
Fredrik, in dialysis, is given a copy of Lisbeth's autobiography, and is told that none of it can be proven.
Meanwhile, Erika has been receiving anonymous, violently pornographic hate mail, which causes an uproar in the office.
In prison, Lisbeth is interrogated by the prosecutor, and says nothing.
Annika is given Lisbeth's computer and the DVD of her rape, which she watches.
Niederman breaks into an abandoned warehouse, and kills a witness, a random biker.
Erika has been receiving more hate mail, as she and the whole office is being spied on by the Section. Dr. Teleborian meets with Lisbeth, and again remains silent.
Erika's bedroom window has been smashed, and she, in desperation, has called Milton Security. Mikael meets up with the owner, and is informed of this, and that someone had broken into his apartment and smuggled cocaine and cash there. The building owner concludes that they are trying to frame him, since they cannot hurt the newspaper. The police find that Jonas (the Section member Teleborian had met with) had met up with the Nikolic brothers, sharpshooters in the Bosnian War and the ones who are pursuing the members of Millennium.
Mikael decides to meet with Erika at a restaurant names "Samir's Gryta". The police try to warn Mikael that they will attempt to kill them there, but Mikael had left his phone at the office. They call the restaurant, and Mikael, in an attempt to answer the phone, runs into one of the brothers, who pulls out a gun. Mikael fends him off as the police hurry towards the restaurant. Figuerola arrives with the police and recognizes the other brother waiting in a car outside the restaurant, and arrests them both. The Section is dismayed when they find that the two brothers had failed their job.
In court, Lisbeth enters with ear and facial piercings, a mohawk hairstyle, black makeup, and dark clothing. As the court procession proceeds, Mikael decides to print Lisbeth's story in the magazine. Mikael visits Erika, who is being monitored by police, to say that he had gone against her decision to not print the magazine. Teleborian heads into court, stating that her autobiography is merely the product of Lisbeth's supposed paranoid delusions. Annika lashes back by demolishing Teleborian's credibility, where he states that she was restrained at St. Stephen's for around 30 days, when in reality, she had been restrained for 381 days. She uses Lisbeth's word and files from the hospital to prove this. The judge does not accept old files as proof against Teleborian's credibility.
Afterward, Plague follows Teleborian up to his hotel. From the lobby he is able to use wireless internet to hack Teleborian's computer, and catches him looking at child pornography. Plague makes a full copy of the computer, which he soon gives to Mikael, who passes on the information to Annika and the police.
In court, Annika shows the video proving Bjurman raped Lisbeth, and showing her statements of abuse were completely true.
As Annika presents her case for the defense, the police arrest the people involved with the Section and seize their place of operation. She proves that Teleborian had confined Lisbeth to an institution as punishment for setting her father on fire, and that he wants to detain Lisbeth at St. Stephen's once more. Annika calls Mikael to the stand and states that Teleborian had written his psychiatric opinions before he had even been allowed to interview Lisbeth. Then Annika calls Edklinth to the stand, and he states that the opinions were formulated in cooperation with Jonas Sandberg, using his computer as proof. Teleborian is left speechless. Edklinth tells Teleborian he is to be arrested, on charges of possessing over 8,000 items of child pornography, and his computer seized as evidence. After Teleborian is arrested, the court then decides that Lisbeth has no further need to been detained in custody.
The Millennium workers celebrate their victory, with Erika returning to work. Lisbeth is encouraged by Annika to check the property she has inherited from Zala and is led to the warehouse where Niederman was hiding. Niederman attempts to trap her in the warehouse and kill her, but she is too fast for him. Lisbeth uses a nail gun to trap Niederman, nailing him to the floor. She considers nailing him in the head but runs out of nails. Upon leaving, Lisbeth instead phones Sonny and tells the bikers where to find Niederman, and then she calls the police after the bikers arrive.
Lisbeth returns home, Mikael briefly visits her to tell that the motorcycle gang killed Niederman and were arrested soon after. They then have a brief, strained conversation, in which she thanks him for everything, and agrees to stay in touch as he is about to leave.