The story picks up just after the events of The Girl Who Played with Fire, Lisbeth Salander has defended herself against Zala, her father. Zala had shot Salander in the head numerous times. Miraculously, she was able to return the attack with an axe. Zala was struck in the head and several other places but none of these wounds was fatal. Zala, a former Russian spy turned gangster, changed his legal identity to Karl Axel Bodin. However, the change in identity does not hide him from the people who know the truth about him and his past.
Dr. Jonasson treats Lisbeth just like any other patient. The Doctor has never performed a brain surgery to this scale, so he was careful while doing the surgery. Miraculously, he saved Lisbeth and Zala also received the best medical care despite the fact that he is a murderer, ex-spy, who tried to kill his daughter.
While Lisbeth is in hospital care, Mikael Blomkvist is investigating everything he can to prove Lisbeth's innocence. He especially wants to prove that Lisbeth is not a criminal, but a victim.
Mikael has developed a protective attitude over Lisbeth, refusing to share information to the police. He works non-stop in order to prove Lisbeth's innocence and has the support of the Millennium magazine. Mikael also called in his sister for help, Annika, who is an advokat. Zala realizes that his recovery is going to take much longer than he had expected. Even while he is recuperating in the I.C.U., Zala is planning his defense and the disappearance or murder of Lisbeth.
Unfortunately for Zala, his former employer, the Section, has no plans to save him this time. Gullberg, the former director of Säpo's secret division, kills Zala before killing himself.
During the majority of the story, Lisbeth is in the hospital recovering from her gunshot wounds. She has to rely on someone else, for the first time in her life, in this case on Blomkvist, Jonasson, the police and Giannini. With the help of these people, she could be proven innocent of the triple homicide in Stockholm.
While researching, Mikael discovers many of crimes committed by officials in the Section, which is a special division of the police force. The Section is responsible for the crimes Lisbeth is being committed of.
Lisbeth writes her autobiography, a novel that will expose a lot a people, who will be arrested and she got to share her story to the public. After some undercover work exposing the Section, Lisbeth is set free.