Scott and Kelly are in Acapulco and return from a fishing excursion. An attractive woman, Vanessa Pemberly, comes over and starts flirting with Kelly. Realizing where his partner is going to end up, Scott heads for the hotel while Kelly takes Vanessa out for drinks. She suggests that they take a taxi rather than walk and Kelly agrees. However, it's a set up and the driver uses a blackjack on the agent and then gives him a sedative to keep him out.
Vanessa and the driver take Kelly into the hills outside of town to a small building owned by Dr. Zoltan Karolyi. Karolyi has his equipment set up and introduces himself to Kelly when the agent wakes up. Kelly claims he's just a tennis bum but Karolyi knows all about him and boasts that he's well-known as an expert on conditioning. He tells Kelly that they have been preparing for eight months and that once he's done, Kelly will obey him as if he were a god.
Karolyi and his team begin by reflecting light into Kelly's face via spinning mirror. Next they inflict pain on Kelly, isolating his consciousness and depriving him of his identity. They then regress him to age of 9 and recreate a car accident from his childhood using sound effects and a prop car. Karolyi cracks Kelly's ribs with a baton to simulate the damage and then implants false memories that Scott was the driver. They then put Kelly in a fake hospital set and use a mirror to associate his memories of pain and betrayal at Scott's hands with the reflected light.
Kelly wakes up and in the next session, Karolyi and Vanessa play the role of a general and an agent in a fake Washington office. They tell Kelly that Scott is a traitor and that Vanessa is a fellow agent. When Kelly passes out, Karolyi is satisfied that his conditioning is successful, gives the agent memories to account for his two-day disappearance, and has his men return him to Acapulco.
Kelly stumbles back to the hotel and tells Scott that he was in an accident when a produce truck his taxi. Scott informs him that the Pentagon has ordered them to recover propaganda material that a man named Rubez is producing locally for distribution to neighboring companies. Kelly takes his partner's gun and casually holds it, then gives him back to him. When Scott notices that Kelly appears distracted, Kelly insists that he's fine and says that he'll go to the warehouse while Scott checks out Rubez's home.
At the warehouse, Kelly finds the propaganda materials but Vanessa is waiting and uses the mirror to entrance him. Karolyi and his man Rubez are there and the doctor implants new memories convincing Kelly that Rubez is running a sting for the Mexican government. Kelly is to tell Scott that Rubez is clean and continue suspecting Scott is a traitor.
When they meet back at their hotel room, Scott isn't convinced that Rubez is innocent. An increasingly irritable Kelly snaps at him and refuses to break off his vacation to continue the investigation. Once Scott leaves, Vanessa comes to the hotel and continues to reinforce Karolyi's programming. When Kelly doubts Scott's guilt, Vanessa uses the mirror again and reinforces his conditioning.
That night, Kelly and Scott take Vanessa to a club. Karolyi and his henchman Smollet are at a nearby table and the doctor explains that once Kelly kills Scott in a public place, they will have discredited the American intelligence organization. Vanessa uses her mirror to trigger Kelly's conditioning, and he tries to pour Scott a glass of champagne. When Scott refuses, Kelly pours the champagne on his arm and starts ranting about how pure his partner is. Scott tries to leave and Kelly breaks the champagne bottle and goes after him. The two men fight and Scott manages to knock his partner unconscious.
The next day, local agents Blaine, Greenberg, and Tate meet with Scott. They've confirmed that Kelly was never in an accident like he claimed and they figure that he's either sold out or cracked up. The agents have also learned that Vanessa works with Karolyi and know about his conditioning experiments. The head man, Blaine, warns that Kelly has been conditioned to create an international incident and discredit the organization, and orders Scott to kill Kelly. Scott refuses, warning that if they go after Kelly then they'll have to deal with him as well. Blaine reluctantly gives him forty-eight hours to bring Kelly in before they issue a Code 10: Kill on Sight.
Back at the hotel, Scott gets a call from Kelly, who asks for his help. Kelly claims that he's been drugged but he's recovering, and asks Scott to meet him at the warehouse. Scott agrees and heads up... and Kelly tells Karolyi and Vanessa that he's set up Scott.
At the warehouse, Kelly ambushes Scott and comes after him with a knife. The two men struggle and Kelly screams that Scott is a traitor. However, Greenberg and Tate arrive and Kelly flees rather than risk capture. Scott tells the two local agents what happened and they take him back to their office. Blaine says that termination is the only option but Scott insists that his three years with Kelly should be able to override Karolyi's two days of programming. He points out that Kelly could have killed him twice but didn't and figures that his partner is resisting the conditioning.
Scott goes back to the hotel and takes a call from his mother in Philadelphia. Kelly comes in with a gun and Scott lets his mother finish before hanging up. Kelly forces him to drive to an observation point and orders him to jump. However, Scott refuses saying that if Kelly wants him dead then he'll have to do it himself. Kelly hesitates and Scott tells him that Karolyi has programmed him and he has to fight it. After a moment, Kelly aims the gun and fires, trying to hold his arm steady. The gun waves and each shot goes wild until Kelly runs out of bullets. Scott takes the gun and then stops his partner when he tries to kill himself.
Later, Kelly leads the local agents to Karolyi's hideout. The doctor is happy to tell them what he's done and explains that they don't need to torture him for information because he plans to defect. Vanessa and Smollet are shocked at the betrayal and Vanessa tries to stab her boss with a scalpel. Kelly and Greenberg stop her and have the enemy agents taken away. A disgusted Kelly figures that they'll end up protecting Karolyi as their next assignment.