Hanna Heller is a fifteen-year-old girl who lives with her father, Erik, in rural northern Finland. Since the age of two, Hanna has been trained by Erik, an ex-CIA operative from Germany, to be a skilled assassin. He teaches her hand-to-hand combat and drills her in target shooting. Erik knows a secret that cannot become public, and Marissa Wiegler, a senior CIA officer, searches for him in order to eliminate him. Erik has trained Hanna with the intent that she will kill Marissa. One night, Hanna tells Erik that she is "ready" to face their enemies. Erik digs up a radio beacon that will alert the CIA to their presence. Although he warns Hanna that a confrontation with Marissa will be fatal for either her or Marissa, he leaves the final decision to Hanna, who activates the beacon. Erik leaves, instructing her to meet him in Berlin.
Hanna is seized by special forces and taken to an underground CIA complex where a suspicious Marissa sends a body double to interrogate Hanna when Hanna asks for her by name. While talking to the double, Hanna starts to cry and embraces the double tightly, which makes her captors uneasy. They send guards to her cell to sedate her. As they enter the cell, Hanna kills the double along with some of the guards and escapes, discovering that she is in Morocco. Hanna meets Sebastian and Rachel, who are on a camper-van holiday with their children, Sophie and Miles, by chance. She stows away in the family's camper-van on the ferry to Spain, seeking to reach Berlin. The family is kind to her, and she and Sophie become friends: she tells Sophie about the Berlin rendezvous and they even share a kiss.
Marissa hires Isaacs, a sadistic former agent, to capture Hanna, while other agents are searching for Erik. Marissa kills Hanna's maternal grandmother after failing to learn anything useful from her. Isaacs and two skinheads have discovered from the Moroccan hotelier with whom Hanna stayed about the family and trail them, cornering Hanna and the family, but she manages to escape after a vicious fight. Marissa interrogates the family and discovers that Hanna is heading to Berlin. Meanwhile, Erik fights off an attempted assassination and tries but fails to kill Marissa. Arriving at the rendezvous, Hanna meets Knepfler, an eccentric magician and friend of Erik's, who lives in an abandoned amusement park. Before Erik arrives, Marissa and Isaacs appear. Hanna escapes, but overhears comments that suggest Erik is not her biological father.
Later, Hanna goes to her grandmother's empty apartment where she finds Erik, who admits that he is not her biological father. He once recruited pregnant women into a CIA program where their children's DNA was enhanced in order to create super-soldiers. After the project was shut down, its subjects were eliminated. Marissa and Isaacs arrive; Erik acts as a distraction to allow Hanna to escape. Erik kills Isaacs, but is shot dead by Marissa, who then goes to Knepfler's house finding Hanna, who has just discovered Knepfler, who had been tortured to death by Isaacs. After Hanna flees, she is cornered and kills Marissa
