Pete is at the scene of a murder as a woman reports to the police that two Latin men shot the victim down in the street. Nelson Richardson emerges from the nearby train station, surveys the scene, and whispers to Pete that "it's off" before departing in a taxi.
Later, Pete is at his office when MacGyver comes in with composites of the killers. Pete looks at them and admits he didn't get a very good look at them. He fumbles for his coffee cup and MacGyver notices. Pete then explains that he doesn't have a lot of time and he called MacGyver in to help. Paul Starns from the DXS arrives Pete explains that he's a high-level watchdog with the organization. Starns complains that the Phoenix Foundation has taken on the return of Samantha Lorra to her country of San Pablo to participate in the presidential election and hasn't kept the DXS informed. Pete points out that the DXS refused the Foundation's help and he doesn't feel they need to keep the DXS informed. Starns points out that Pete has a personal relationship with the Lorra family and Samantha herself. Pete objects, noting that he met Samantha 20 years ago just after he became divorced. Starns explains that a death squad killed the man dropping off the videotape evidence confirming the execution of 200 political prisoners in San Pablo. MacGyver asks how the death squad found out about the drop but Starns admits he doesn't know. The DXS man insists that they want to help but they can't publicly do, and Pete explains they need that tape for a six o'clock broadcast that night. The dead man was a courier working for Richardson, who took the tape and left, and Samantha is the only one who knows how to contact him. The Foundation has arranged a safe house for Samantha to stay in until she flies to San Pablo that night. Starns is satisfied with the arrangements and apologizes to Pete before leaving.
Pete and MacGyver take a taxi to the docks to pick up Samantha. MacGyver asks if Pete's eyes are bothering him but Pete insists he's fine. Samantha comes in as part of a freighter crew and gets into the taxi. Pete introduces her to MacGyver and they leave. Pete explains the situation to her and Samantha says she needs a push button phone to contact Richardson. They go to the safe house and Samantha makes the call. When Richardson gets it, he'll call her. As Pete goes to the kitchen, he stumbles over the furniture and gets the wrong type of juice for Samantha. Pete finally admits that he had glaucoma, and he put off treatment for too long because he couldn't admit that he might have the illness. There is a treatment but he could lose his sight. Pete insists he needs MacGyver's help, for Samantha's sake. MacGyver agrees and Pete goes out to Samantha to give her her juice.
Samantha gets a call back from Richardson who arranges a meeting and wants the person making the pickup to wear a dove pin that Richardson gave her last year. MacGyver puts the pin on and leaves. The death squad killers, Cardosa and Ramos, are watching the safe house and recognize MacGyver from the docks. They figure that once they have the tape, they can dispose of MacGyver and Samantha.
MacGyver arrives at the train station for the rendezvous, unaware of the men following him. He meets Richardson, who says he'll take him to the rail cat where he hid the videotape. As they go, MacGyver notices that Richardson is limping and the man explains that he was a journalist and wrote an editorial when the death squads killed Samantha's father. They crushed his foot and tortured him.
At the safe house, Pete is taking medicine for his eyes and drops the pill. Samantha finds him as he's crawling on the floor trying to find it. He snaps at her and then apologizes, Samantha admits that she knows he has a problem with his eyes and offers to listen to whatever he has to say. Pete admits he's having a tough time coming to grips with his condition.
Richardson and MacGyver go to the rail car and the journalist explains that he promised Samantha's father that he wouldn't let anything happen to her. They discover that someone has moved the rail cat and start looking. Richardson finds the car but Cardosa and Ramos come searching for them. MacGyver makes a crude muzzle-loading gun out of a steam hose and has Richardson shoot rocks into the air to draw the killers' fire while MacGyver gets the tape. Cardosa and Ramos don't find anything and go back to search the railroad cars. As they close in on MacGyver, Richardson uses the steam hose to shoot a metal rod at the killers and then grabs a rectangular chunk of rock to convince them he has the videotape. He runs away from the rail car and MacGyver gets the tape and sees Richardson run by. He can only watch helplessly as Cardosa guns down Richardson and discovers he didn't have the videotape.
MacGyver takes the tape to the Jerico broadcast studio and they prepare to put it on the air. Pete gets word and waits for MacGyver to call. He embraces Samantha for a moment and then they awkwardly separate. Samantha insists that he don't hide her condition from her and reminds him that they once shared everything. Pete remembers how they spent time just looking at things and now he can't.
Cardosa and Ramos arrive at Jerico and realize that they were tricked. They figure that the news won't benefit Samantha if she's not around to be a candidate. They can't kill her because it will turn her into a martyr, so Cardosa plans an accident for her.
Pete admits to Samantha that he's not sure if he can handle being unable to do his job. He's also not sure if he can face the possibility of total blindness if the surgery fails. Samantha admits that she was paralyzed with fear when she had to face the choice of running for President and possibly dying the way her father did. She committed to what she could do and felt free as a result. Pete admits that he's not at that point yet.
At the studio, MacGyver watches the broadcast of death squad massacres of innocent civilians. He gets word that Pete called and calls the safe house to let them know that the tape went on the air but Richardson died. Someone cuts the phone line as MacGyver claims he knows who leaked their plan. At the house, Pete realizes someone has cut out the power and sends Samantha to the kitchen to get matches. A black-clad figure comes in and captures Samantha, and then distracts the nearly blind Pete as he stumbles in the dark. The intruder tells Samantha to make it easy and Pete recognizes his voice. The intruder knocks Pete out and leaves.
A few minutes later, MacGyver arrives. Pete blames himself for failing to protect Samantha and explains that he recognized Starns' voice. MacGyver has already figured out that Starns had him followed. When they wonder why Starns left Pete alive, Cardosa arrives with a gun to explain that Pete was left there as bait. He takes Pete and MacGyver to a hangar at the airport where Starns is keeping Samantha. Starns plans to set an "accidental" fire and let the Foundation take the blame for being careless. Starns insists he's killing Samantha to protect the U.S. and keep the region from exploding into chaos. He lights a piece of canvas stuffed into a gas can and departs. As the fire burns down, MacGyver has Pete stand up so they can move to a grinder and cut their ropes. MacGyver grabs the flaming can and throws it into a dumpster but it explodes prematurely as he tries to close the lid. MacGyver's hands are badly burned and the flash blinded Pete. They only have a few minutes until Cardosa and the others realize their plan failed.
MacGyver gets to the door as Starns, Cardosa, and Ramos realize something is wrong. MacGyver has Samantha bolt the door with a crowbar. Working together, Pete and MacGyver push a wheeled workbench against the door to block the window so no one can shoot in. As the three men grab an I-beam to ram the door, MacGyver has Samantha find some cable cutters while he has Pete drive a GPU tug cart. MacGyver will function as his eyes and Pete as his hands. Pete drives the cart and rams a plane. They argue briefly and then start over. As the trio starts breaking the door down, MacGyver directs Pete to drive the tug to the workbench. Pete puts it in neutral while Samantha gets the cable cutters and has her cut a power cable on the tug. MacGyver then has her hook the cable up to the door the killers are trying to break down. Finally she cranks the amps up as high as possible and throws the switch. The beam hits the electrified door, shocking Starns and the others. Samantha grabs the gun and takes the men prisoner.
Later, the medics take care of MacGyver and Samantha thanks him for his help. She then goes to Pete and promises to pray for him. Pete wishes her well and says that he plans to go through with the surgery. She insists she's stay alive and win the election if he survives and comes to see her. Pete agrees and Samantha departs for San Pablo. As the two friends ride off, Pete asks if MacGyver wants to go bowling.