Hanna Heller (Saoirse Ronan) is a 17-year-old girl who lives with her father, Erik Heller (Eric Bana) in the wilderness of Finland. Ever since she was two years old, Hanna has been trained by Erik to become an assassin. As part of her training, she has never come into contact with modern technology and has memorized a series of fake back stories for herself to be used "when the time comes".
One night, Hanna tells Erik that she is "ready", and he gives her a box containing an old transmitter that will alert the outside world to their presence. After analyzing the situation, Hanna flips the switch, sending a signal of her location to Marissa Wiegler (Cate Blanchett), a corrupt CIA agent. Wiegler sends a team to Erik's cabin, where Hanna, who had been waiting for them, is captured and taken to a CIA safe house in Morocco. There, she discovers that Erik is a former CIA agent who betrayed the agency and knows a secret that can't become public. Wiegler has been assigned to kill him, but Erik has trained Hanna to kill Wiegler. Knowing that Hanna was captured too easily, Wiegler sends a body double (Michelle Dockery) to speak with Hanna. Hanna kills the double, breaks free and escapes the compound.
While on the run through the desert, Hanna meets Sebastian (Jason Flemyng) and Rachel (Olivia Williams), and befriends their daughter Sophie (Jessica Barden). They decide to help her go to Berlin, after she tells them her fake back story. Meanwhile, Wiegler hires a mercenary called Isaacs (Tom Hollander) to capture Hanna while she goes after Erik, who is in Germany. Later, Isaacs and his men corner Hanna and the family, but she manages to escape after killing one of Isaacs' men. The son of the captured family, who has a crush on Hanna, is tricked into telling Wiegler that Hanna is heading for Berlin.
In Berlin, Hanna meets with one of her father's associates, who lives in an abandoned amusement park, to rendezvous with her father. However, Wiegler and Isaacs locate them and kill Erik's associate, but Hanna escapes. She eventually meets with her father at her grandmother's apartment, where she discovers that Wiegler has murdered her grandmother. Hanna learns that Erik is not her father, and it is revealed that Erik was once a recruiter for a program in which pregnant women were recruited from abortion clinics so that the CIA could alter their children's DNA, enhancing their strength, stamina, and reflexes while suppressing emotions like fear and empathy in order to create a batch of super-soldiers. The project was deemed a failure by the CIA higher-ups and all the women and their genetically-modified children were eliminated. Erik tried to escape with Hanna and her mother, but Wiegler murdered Hanna's mother before Erik could escape with Hanna to their cabin.
As Erik finishes explaining the truth to a bewildered Hanna, Wiegler and Isaacs arrive, intent on killing them; Erik acts as a distraction to allow Hanna to escape. Erik kills Isaacs and his cohort, but is shot and killed by Wiegler, who then chases Hanna back to the abandoned amusement park. Hanna pleads for an end to the killing, but Wiegler shoots Hanna, who in turn wounds Wiegler with an improvised bow-and-arrow. As Wiegler attempts to flee, Hanna hunts her to the top of a tall slide; a disoriented Wiegler fall down the slide, dropping her gun. Hanna picks up the gun, commenting how she missed Wiegler's heart, and shoots her dead.