The police arrive at the train station to investigate the death of a man. A woman identifies the two killers as well-dressed Latin men. Pete Thornton is in the crowd, watching the entire thing. A man, Nelson Richardson, emerges from the train station, whispers to Pete that their meeting is off, and quietly slips away in a taxi.
Later, MacGyver delivers composite sketches of the killers to Pete at his office. As they talk, MacGyver notices that his friend is having trouble seeing things in his peripheral vision such as his coffee cup and his telephone switchboard. Paul Starns of the DXS comes in and complains that the Foundation isn't keeping his organization informed on the security procedures for Samantha Lorra. Samantha Lorra is the daughter of the former president of San Pablo, and is running for the office since her father's assassination at the hands of a death squad. Pete insists that since the DXS refused to safeguard Samantha, he arranged for the Foundation to do so. Starns points out that Pete has a personal relationship with Samantha and Pete admits that he and Samantha had a brief affair 20 years ago after his divorce, but it's over and it has no impact on his decision now.
Starns explains that the dead man at the train station was a courier delivering a videotape of death squad atrocities against innocent civilians. The Foundation plans to work with Jerico Broadcasting to air that tape, but they need it by 6 p.m. that night to make the evening news and expose Samantha's political rivals in the election. The courier had the tape and was working with Richardson, who managed to get the tape before the murder but couldn't risk turning it over to Pete. MacGyver wonders how the killers, death squad members, managed to learn about the drop but Starns admits he doesn't know. Samantha is the only one who knows how to contact Richardson and the Foundation is putting her in a secure safe house. Samantha will be flying back for the election that night and they need the videotape to air by then. Starns apologizes for insinuating Pete was less than professional and takes his leave.
Pete and MacGyver pick up Samantha at the docks where she's being smuggled into the country among the crew of a tramp freighter. She and Pete share a brief reunion, and then she explains she needs to call Richardson and leave a message to arrange for the drop-off of the videotape. They go to the safe house and Samantha makes the call. Meanwhile, Pete goes to the kitchen to get some juice and stumbles into furniture. As he pours the wrong type of juice, MacGyver comes in and asks what's wrong. Pete finally admits that he had glaucoma. When his friend wonders if there's a cure, Pete admits that he was too proud to admit a problem and now it may be too late. The only treatment now could work, but could also permanently blind him. Pete asks MacGyver to stay on the case to protect Samantha because he can't any more and MacGyver agrees.
Richardson calls back and arranges a meeting at the train station. He tells her to have the person making the pickup wear a dove pin he gave her. Samantha gives MacGyver the pin and he goes to the train station. He's unaware that the two killers, Cardosa and Roma, already know where the safe house is and are watching him. They follow him, planning to get the tape and dispose of everyone once they have it.
At the station, MacGyver meets with Richardson. He explains that he hid the videotape in a rail car and leads MacGyver to it. As they go, MacGyver notices that the man has a limp. Richardson explains that he was a journalist and ran an editorial on the death squads after they killed Samantha's father. They responded by arresting him, crushing his foot, and torturing him for weeks before releasing.
At the safe house, Pete tries to take some pills for his condition but drops the medicine. Samantha finds him crawling on the floor and he snaps at her. Shocked and angry, she goes into the next room and Pete goes after her to apologize. Samantha says that they used to be able to talk to each other about anything and insists that he talk to her about his problem. Pete admits that he's having trouble handling his new handicap.
Richardson realizes that someone has moved the rail car. He and MacGyver fan out to look for the car and finally locate it. Cardosa and Ramos come looking for them and MacGyver rigs a steam hose to use as a muzzle-loading gun. He goes into the rail car to get the videotape while Richardson fires rocks at a distance, drawing the killers away. However, when they don't find anyone and return to their search. With time running out, Richardson fires a metal rod at them, picks up a rectangular chunk of paving, and runs away. The killers spot him and, assuming he has the tape, chase after him. In the rail car, MacGyver finds the videotape but can only look on as Cardosa kills the helpless Richardson, only to realize the journalist doesn't have the tape.
MacGyver escapes and gets to the Jerico broadcasting company. They call to notify Pete that they have the tape and will be airing it. He embraces Samantha in celebration for a moment and then the two of them awkwardly withdraw. Samantha wants him to talk about what he's feeling and Pete admits that he remembers how they once spent time looking at things, but he's no longer able to do that with her.
Cardosa and Ramos drive to Jerico and realize that they're too late. However, Cardosa figures that if they dispose of Samantha before she leaves for San Pablo, it won't make any difference. All they have to do is make her death appear accidental so she doesn't become a martyr.
At the safe house, Pete admits to his old flame that his greatest fear is that he'll no longer be able to do his job. Also, he's afraid of going through with the surgery if the result is total blindness. Samantha sympathizes and explains that she felt much the same way when she had to choose to run for president and possibly die the same way that her father did. In the end, all she could do was commit to doing what she had to. As a result, she felt much freer. Pete admits that he isn't sure if he has her courage.
MacGyver and the broadcast team watch as the videotape goes out on the air. He follows up on the studio's call to Pete and calls to let his friend know the tape aired. As MacGyver tells Pete that Richardson died and he knows who leaked their plan, a black-clad intruder cuts the phone and power lines. Pete sends Samantha to the kitchen but the intruder captures her. In the dim light, Pet is helpless. The intruder tells Samantha to stop struggling and make it easy for herself and Pete recognizes the voice. The man knocks him out and leaves with Samantha. MacGyver arrives a few minutes later and Pete tells him that the man who betrayed them and abducted Samantha was Starns. MacGyver had already deduced the same thing. When they wonder why Starns left Pete alive, Cardosa arrives and informs them he did it so they'd have bait to capture MacGyver.
Cardosa and Ramos take MacGyver and Pete to an airport hangar where they plan to fly out of the country once the murders are done. Starns is holding Samantha prisoner and has set up fuel cans for the "accident." As they tie up Pete and MacGyver, Starns explains that he plans to dispose of Samantha and blame the Foundation for not properly safeguarding her, leaving him in the clear. When MacGyver wonders why he's betraying his country, Starns insists that he's killing Samantha to keep her from destabilizing the region and plunging both San Pablo and the U.S. into a political morass. He lights a piece of canvas placed in a gas can and leaves with the other two men.
Once the killers are gone, MacGyver and Pete work together to jump over to a grinder and cut their ropes loose. MacGyver gets free, grabs the burning gas can, and throws it into a dumpster before it sets off the fuel. As he tries to close the lad, the gas explodes, badly burning his hands and blinding Pete. They realize they only have a few minutes before Starns realizes something is wrong and comes back to finish them off.
Unable to close his hands, MacGyver has Samantha bolt the door just as the trio comes back. Pete and MacGyver shove a cabinet in front of the narrow window to keep them from shooting in, and Cardosa and the others go to find an I-beam to batter down the door. With time running out, MacGyver gets into an airplane tug cart with Pete. He directs Pete which way to go, acting as his friend's eyes while Pete provides his hands. After a few near mishaps, they manage to get the tug cart over to the cabinet. MacGyver has Samantha cut the power cables and attach them to the door. When Starns, Cardosa, and Ramos slam the I-beam into the door, MacGyver has Samantha turn on the power. The resulting shock stuns the three men long enough for them for Samantha to grab a gun and take them prisoner.
Later, the authorities take away Starns and the others while the paramedics tend to MacGyver's hands. Pete and Samantha exchange a final farewell and she wishes him well. Pete says that he plans to go through with the surgery no matter what might happen. Samantha offers him a deal: they both promise to stay alive and will meet again. Pete agrees and watches as she leaves for San Pablo.