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.
Lisbeth Salander purchases an apartment in Stockholm. On returning to Sweden after nearly a year living abroad, Salander reconnects with her best friend and former partner Miriam Wu and offers her free use of her old apartment in return for forwarding her mail. Later, Salander confronts Nils Bjurman after hacking into his mail and discovering that he has an appointment booked with a tattoo removal specialist. Threatening him with his own gun, she warns him not to remove the tattoo that she etched on his abdomen.
The film begins at the conclusion of The Girl Who Played with Fire (film). 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.