We see a man (Jai Courtney) setting up his rifle, and he stands outside a building, getting a clear view of the people at a distance. With the sniper lens, he scopes out the area for civilians. He begins to open fire on seemingly random people. He kills five people and then leaves.
Police arrive at the scene and collect evidence, including a quarter from a parking meter and a bullet shell. They eventually come to a man named James Barr (Joseph Sikora), and they apprehend him. Detective Emerson (David Oyelowo) interrogates him, and we see it is not the same man who did commit the shootings. Emerson tells Barr that he (Emerson) and DA Rodin (Richard Jenkins) are deciding on whether to give him life in prison or put him on death row, but it all comes down to his confession. Instead, Barr writes down on a piece of paper in big letters - "Get Jack Reacher." Emerson asks "Who the hell is Jack Reacher?"
He learns that Reacher was a military man, but there is a great deal of mystery surrounding him, and he cannot be found unless he wants to be found...at which point, Emerson and Rodin are told that Jack Reacher (Tom Cruise) is there to see them. Their initial meeting is uneasy, to say the least, and we see that Barr is in the hospital in a coma after being assaulted by other prisoners. His attorney, Helen Rodin (Rosamund Pike), the DA's daughter, comes in and tells the men that she doesn't want anyone talking to Barr without her being there, unaware of what's happened. Nobody, not even Reacher knows why Barr asked for him, because Reacher has no real connection to him.
We see that Reacher and Helen meet up later at a diner. Helen is set to prove Barr's innocence, but Reacher claims that Barr fits the bill for the type of person to commit these murders. Barr was also a military man, and after a certain period of time, he ended up killing four men during his time in Kuwait City, but he was let go on a technicality. It turns out these men were part of a "rape party" and they assaulted about 28 women. With this knowledge, Reacher tells Helen to find out more about the victims.
Helen visits the father of one victim. He is very distraught, and he tells Helen that his daughter was a good person, and he can't understand why Helen is trying to prove Barr's innocence. He intimidates Helen to the point where she runs out the door. Meanwhile, Reacher goes to the building where the sniper fired upon the civilians, and tries to get a better idea of how everything went down. He meets with Emerson later, who asks him about the serial number on the shooter's rifle, but Reacher just asks him about the year on the quarter found at the parking meter, which is 1968.
That night, Reacher goes to a bar alone. He is approached by a pretty young girl named Sandy (Alexia Fast), who appears to be propositioning Reacher. He rebuffs her, implying she's a hooker. She gets angry and has a group of her "brothers" come to her defense. They challenge Reacher and fight him outside, but he effortlessly takes down most of them. Almost immediately, the police arrive on the scene and apprehend Reacher. He looks at the leader of the group and asks "Who sent you?"
Helen and Emerson get Reacher out of custody. She tells him what she's learned about the five victims - the first victim, Chrissie Farrior, (the one whose father she visited) was a nanny for a young girl. She was going to leave to China a week earlier, but the girl wanted her to stay for her 7th birthday, and they went into town that afternoon to shop for a birthday dress. The second victim she learned about, Rita Coronado, was a mother who would always drop her honors student son off to school. The third victim, Nancy Holt, was shopping for a watch for her husband for their anniversary. She didn't want the purchase showing up on her credit card so she can surprise him. The fourth victim, Oline Archer, was running her husband's construction company after his death, even though she didn't approve of it. When given a chance to sell, she refused. She went into town to secure a loan. The last victim, Darren Sawyer, had gotten into a fight with his wife before he died. He was found next to a bouquet of roses on a bench.
Reacher remains cynical and assumes that Sawyer and Holt were having an affair based on how it was described that she walked toward him before he was shot, and then continued walking with shock. This adds to his whole notion that not every victim is innocent. He also tells Helen that he knew Sandy was set up, because he didn't believe any random girl would proposition him and that she most likely knew who he was, so he used a fake name (Jimmy Reese).
We cut to a meeting in a dark area between a guy who's been following Reacher, and the actual shooter, whose name is Charlie. We also meet the boss, who is only known as "The Zec" (Werner Herzog). We learn that only one of the victims was intended, and the rest were shot to cover this up. The first goon is being hassled by Charlie and The Zec about his loyalty after they get into an argument, and The Zec reveals that he bit off his fingers at one point to survive frostbite and gangrene. He orders the goon to do the same to prove his loyalty, but he can't, so Charlie shoots him. Charlie asks The Zec what they should do about Reacher, to which he replies "what we always do."
Reacher goes to the workplace of Sandy, where he learns that she was set up by the guys to lure him to them. She gives him a name, Jeb (the leader of the group), and gives Reacher the keys to his car. She appears to be coming onto him again, but Reacher tells her to get out of town.
He drives to Jeb's home and sees a catatonic woman sitting in a rocking chair. He asks if Jeb is home, but she doesn't respond. When he goes into the house, she takes out a phone and presses a button. As Reacher looks around, he is ambushed by two incompetent goons. They struggle to actually hit him after the first time, so he easily takes them down. A third guy almost shoots him, but Reacher disables him and also takes his car to look for Jeb.
Reacher meets up with Helen again and notices that a silver car has been following him all day. He also learns that Jeb was killed after being released from prison. They also realize that one of the victims was intended, and they learn that it was Oline Archer, and that the killers were working for Lebendauer Enterprises, a rival company. Reacher decides that Barr might very well be innocent.
We see Sandy about to go out for the night. As she walks out, she is approached by Charlie. They knew each other through Jeb. He invites her out for a drink, but she passes. After that, one of Charlie's goon friends punches her hard across the face, and Charlie finishes her off by suffocating her.
The next morning, Helen catches Reacher leaving the building where she works. He tells her that now that she is involved in this case, she could be killed, but she should not be scared.
Police later find Sandy's body behind the motel where Reacher is staying. Reacher drives up to the scene and sees her being carried away. He is visibly upset. Emerson sees him and tries to arrest him, but Reacher drives off and he is pursued by Charlie and the police. He manages to get them off his back as he hides out in a crowd after quietly and safely escaping the moving car.
Later, Helen is meeting with her father and Emerson. She gets a phone call from Reacher, and he tells her two things - one, he took her car, and two, he thinks either Rodin or Emerson are in on the scheme.
Reacher goes to a shooting range to gather some more information. He meets a man named Cash (Robert Duvall) and thinks he might gather more information on Barr, since he was Cash's best shooter. Cash will only tell Reacher anything if he proves himself a good shooter on the field, which he does. He is allowed to view security footage of Barr's visit, and he sees that Charlie came with him. Reacher recognizes him as the guy in the silver car who was following him.
Sometime later, Helen talks to her father about the evidence surrounding the case that would prove Barr's innocence, but Rodin is skeptical. This makes Helen suspicious, thinking it is her father who is the mole. He tells her that he really does care about her, and that he wants to put her in protective custody, but she refuses. As she leaves, she gets into an elevator, but Emerson gets in. After a brief moment, he pulls out a taser and incapacitates her. She is taken by Charlie and the other goon.
Reacher is at a bar again, and he calls Helen's phone. Charlie answers and threatens her life. Reacher swears that if Charlie does anything to Helen, he will show him no mercy.
Reacher meets up with Cash after they learn where the villains are. Reacher drives Helen's car without being seen to avoid getting shot while Cash aims for the other shooters who already begin opening fire upon him. They manage to kill the other goons, and Reacher catches up to Charlie. He gets him to put his gun down, but Reacher also tosses his away and they engage in hand-to-hand combat. Charlie puts up a good fight, but he is ultimately taken down, and Reacher presumably breaks his neck.
He gets into the trailer where Emerson and The Zec are keeping Helen. Emerson prepares to shoot, but Reacher knows he is there. Reacher knows Emerson planted the quarter at the parking meter. Emerson shoots at Reacher, but he easily shoots Emerson down. Helen is released while The Zec just sits in the back. Reacher knows "zec" means prisoner, and The Zec believes he can escape prison in America easily. As Helen calls the police, Reacher shoots The Zec in the head. Helen asks him "What about bringing them to justice?" to which Reacher responds "I just did." With everyone dead, she doesn't know how to prove Barr's innocence, but Reacher has faith in her. He leaves with Cash just as the police arrive.
Helen visits Barr in the hospital as he wakes up. He believes he really is guilty of the murders, and he breaks down in tears. Helen asks him how he would've committed the murders, and according to what he tells her, it's enough for him to prove his innocence. He is still afraid and wants to be protected, and when she asks why he needs protection, he mentions a cop who would stop at nothing to do what is right. And yes, he means Reacher.
As he is telling her this, we see Reacher sitting at the front of a bus, while in the back, a man is yelling at his girlfriend, and we hear him slap her. After a moment, Reacher gets up and moves to the back, and whatever he's about to do next is left to our imagination.
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