In December 2002, Mikael Blomkvist, publisher of Millennium magazine, loses a libel case involving allegations that he published about billionaire financier Hans-Erik Wennerström. He is sentenced to three months in prison. Lisbeth Salander, a surveillance agent and hacker, is hired by Henrik Vanger, the patriarch of the wealthy Vanger family, to investigate Blomkvist. Vanger then hires Blomkvist to investigate the disappearance of his niece, Harriet, who vanished on Children’s Day in 1966. Vanger believes that Harriet was murdered by a family member. Henrik explains that his brothers- Gottfried, Richard, and Harald- were all supporters of the Nazi regime. Richard died during the war and is not a suspect for Harriet’s murder. Gottfried is described as having been in the Hitler Youth, an aggressive alcoholic whose marriage to Harriet and Martin’s mother was cold and toxic, and the two lived separately with the children living with their father. Henrik also says that he ‘never saw anyone be a worse mother than she was to Harriet’. Gottfried died one year before Harriet disappeared by accidentally drowning in a lake, and Henrik then took responsibility for Martin and Harriet. Harald is a recluse who still holds strong Nazi views and is a suspect for the murder as is Harriet’s mother and all the other family members who were present on that day. Henrik also shows Blomkvist a room whose walls are covered with pressed flowers. The first ones were gifts from Harriet, and since her disappearance, a flower has arrived each year from different places around the world. Henrik believes that Harriet’s killer is sending them.
Salander, who was ruled mentally incompetent as a child, is appointed a new legal guardian, Nils Bjurman (Peter Andersson), after her previous guardian suffers a stroke. Bjurman makes it clear to Lisbeth that unless she co-operates with him he will make her life very difficult and threatens her with incarceration in a mental hospital. Bjurman takes over control of Lisbeth’s bank account so that she has no access to her own money. Lisbeth lies to Bjurman about the nature of her work by pretending that she is just an office assistant.
Lisbeth is attacked by a group of drunk thugs in the subway. Although she manages to fight them off, her laptop is broken. She visits a hacker friend of hers, ‘Plague’, who can save the hard drive and let her use his spare PC, but Lisbeth needs to get a replacement laptop. She goes to see Bjurman who forces her to perform fellatio on him in return for the money that she needs to buy a new computer but he withholds the full amount she needs. Lisbeth calls him again the next day, but at the meeting with Bjurman, he handcuffs her to his bed, beats her, and rapes her. Lisbeth secretly recorded the encounter. She later returns to Bjurman, uses a taser to incapacitate him, ties him up, rapes him with a dildo, shows him the hidden camera footage, explains what Milton security really does, and tells him that she is taking back control of her money and life. If any ‘accident’ happens to Lisbeth, then the film will be released, and any threat to her will result in the same outcome. She then uses a tattoo machine to brand Bjurman’s abdomen with the message “I am a sadist pig and a rapist”.
Blomkvist moves to a cottage on the Vanger estate and meets the Vanger family, including Harriet’s brother Martin, who is the head of the Vanger group, and cousin Cecilia. Martin is congenial and has Blomkvist over for dinner; he and Cecelia both think that Harriet simply ran away as she was unhappy at home.
Inside Harriet’s diary, Blomkvist finds a list of five names alongside what appear to be phone numbers. He visits retiring police inspector Morell, who informs him that his investigation team had been unable to decipher them. After viewing photographs taken during the Children’s Day parade, Blomkvist sees Harriet’s facial expression change suddenly just before she leaves and, after obtaining photographs taken from the same side of the street as her, comes to believe that Harriet may have seen her murderer that day.
Using her access to Blomkvist’s computer, Salander learns that the numbers in Harriet’s diary are references to verses in the Book of Leviticus and emails Blomkvist anonymously. Blomkvist figures out that Salander sent the email and hires her as a research assistant. Together, Blomkvist and Salander connect all but one of the names on Harriet’s list to murdered women. They are all Jewish names, which intrigues Blomkvist, as the Vanger family has a long history of antisemitism. During the investigation, Blomkvist and Salander become lovers.
They suspect Henrik’s reclusive brother Harald to be the murderer, as the two other Vanger brothers had already died by the time that Harriet disappeared. Salander searches through Vanger’s business records to trace Harald to the crime scenes, while Blomkvist breaks into Harald’s house, believing it to be unoccupied. He discovers many Nazi texts and memorabilia amid the wreckage of the interior of the house which has been left to decay. When Harald attacks Blomkvist, Martin appears and saves him. Harald insults Martin for stopping him from shooting Blomkvist. Martin escorts Blomkvist to his home, where Blomkvist reveals what he and Salander have uncovered. Martin says that he’ll call the police, but instead he drugs Blomkvist. Salander’s search of the company accounts points to Martin and his late father, Gottfried, as having been jointly responsible for the murders. She returns to the cottage to find Blomkvist missing.
Blomkvist wakes to find himself bound in Martin’s cellar. Martin explains that Gottfried began teaching him to rape, torture, and kill as a teenager, and Martin boasts about raping and murdering women for decades since his father’s death. However, he denies killing Harriet, insisting that she disappeared. He also says that Gottfried was too theatrical and that leaving the bodies out to be found was a step too far as it drew too much attention. As Martin is in the process of hanging Blomkvist, Salander appears and attacks Martin with a golf club. While she frees Blomkvist, Martin flees in his car. Salander gives chase on her motorcycle. When Martin drives off the road, Salander finds him still alive but trapped in the vehicle. As the car goes up in flames, she makes no attempt to save him.
Blomkvist realises that Cecilia’s late sister Anita was the near-double of Harriet and that some of the film taken on the day of Harriet’s disappearance shows Anita, not Harriet as previously thought. Blomkvist and Salander discover that Harriet has been using Anita’s name and is still alive in Australia. Blomkvist flies there to look for her, and he persuades her to return to Sweden, where she is reunited with her uncle. Harriet explains the truth about her disappearance: that her father and her brother had repeatedly raped her; that she killed her father by drowning him, which was witnessed by Martin; and that her cousin Anita had smuggled her away from the island after Martin returned from school. Harriet notes that her brother was harsher to her than her father and that she knew that remaining on the island would lead to her death at her brother’s hands. As a way of letting Henrik know that she was alive, Harriet sent the pressed flowers as a signal that she was out there in the world. She apologises for frightening Henrik as he had misinterpreted these messages but Henrik reassures her by explaining that thanks to her messages the truth has come out.
Salander’s mother, living in a nursing home, apologises for not choosing a “better papa” for her. Salander then visits Blomkvist in prison and gives him new information on the Wennerström case. From prison, Blomkvist publishes a new story on Wennerström in Millennium which ruins Wennerström and makes the magazine a national sensation. Wennerström is then found dead presumably by suicide. His offshore bank account in the Cayman Islands is raided, and the police suspect a young woman caught on CCTV, whom Blomkvist recognises as Salander in disguise. The film ends with Salander, dressed in disguise as she exits her car, walking along a sunny beach promenade.