While Jack Reacher was intended to be a tent-pole for a film series, a sequel was initially reported to be unlikely due to its lackluster run at the North American box office. In addition, Lee Child, author of the Jack Reacher novel series, makes a brief appearance as a TSA agent.
The Hunter and his men chase Samantha through the streets of New Orleans to lure Reacher into a confrontation. They learn that Harkness framed Turner, who had been investigating his activities, for the murders of the two soldiers who had discovered that Harkness was selling weapons to insurgents, then smuggling opium into the United States. Before Turner can be rearrested, Reacher opens up one of the weapons and dumps out bags of pure opium. Espin finds antitank weapons, though, as declared in the flight manifest. Reacher, Turner, and Espin, acting on information from Prudhomme, intercept a shipment of weapons due to enter the country, where they confront Harkness and his men, and accuse them of corruption. Parasource's CEO, General James Harkness, sends the Hunter to capture Samantha after she uses a stolen credit card to purchase food.
Reacher contacts Turner's friend, Captain Anthony Espin, to move Prudhomme into custody, but they are ambushed by assassins and Prudhomme is killed, while Reacher rescues a wounded Espin and finds out that the assassins are Parasource contractors. Reacher and Turner find Prudhomme in a derelict warehouse filled with drug addicts, and learn that Prudhomme is connected to Parasource, a private military organization that is trying to cover up the murders. En route, Reacher admits to Samantha he might be her father. The trio goes to New Orleans in search of Daniel Prudhomme, the only eyewitness to the murders for which Turner has been framed. They make a quick exit, during which Samantha steals credit cards from one of the students. The three travel to Turner's old private school for protection, but discover that Samantha has her mobile phone with her, which the enemy has likely tracked. Reacher and Turner uncover surveillance pictures of Samantha and surmise she is in danger, arriving at her home to find her foster parents dead and Samantha hiding. The Hunter, revealed to be working with Morgan, later kills Morgan and again frames Reacher. They go to Morgan's house, having deduced he is involved in the conspiracy, and extract information. When two hitmen arrive, Reacher neutralizes them, then escapes with Turner. Reacher is arrested and transported to the prison where Turner is being detained. Moorcroft is later killed by a SOCOM former operator-turned mercenary known as the Hunter, framing Reacher for the murder.
Reacher tries to reach out to Samantha, but she rebuffs him. Moorcroft also reveals an old acquaintance of Reacher's, Candice Dutton, has filed a paternity suit against him, claiming he is the biological father of her 15-year-old daughter, Samantha. Turner's attorney, Colonel Moorcroft, reveals that some evidence shows that Turner is involved in the murders of two soldiers in Afghanistan, but Reacher believes she is being framed. He learns from Colonel Sam Morgan that Turner has been accused of espionage and detained. After busting a human trafficking ring on US Army land, drifter and former Army military police officer, Jack Reacher, returns to his old military headquarters to meet Major Susan Turner, holding his former command, with whom he has been working by phone during his travels.