MacGyver returns home only to discover that everything in his apartment is missing. The thief has left him a copy of Robert Louis Stevenson's Kidnapped and a note telling him to come to Hangar 13 at the airport. MacGyver realizes there's only one person with that twisted a sense of humor: his old friend Jack Dalton.
MacGyver goes to the airport and spots an open side door. Figuring Jack is up to his old tricks, MacGyver uses a cardboard tube to unscrew the bulb from the overhead light and push the door open. A bucket of water falls down. MacGyver goes inside and the lights come up, revealing all of MacGyver's furniture and belongings. Jack reveals himself up on the rafters, and an angry MacGyver tells him to get down. Jack seemingly falls only to reveal he has a rope tied around his ankles. MacGyver finally cuts him down, letting him fall the remaining short distance. Jack explains that he now owns an air freight business and is involved with shipping orchids out of the Central American country of Dinato. He hired botanists to help him, but the Dinato authorities arrested them and Jack needs MacGyver's help to rescue them. MacGyver notices that Jack's left eye is twitching: a giveaway that he's lying. When MacGyver prepares to walk away, Jack admits that he's dying and wanted to do one good thing before he died. His eye doesn't twitch and MacGyver believes him.
MacGyver puts in a call to Pete who confirms that American botanists in Dinato have gone missing. MacGyver and Jack take off in Jack's plane for Dinato. As they fly south, MacGyver notices that Jack is flying without charts, and not doing particularly well. In the map box MacGyver finds some old photos of himself and Jack along with their friend, Michelle "Mike" Forrester. MacGyver remembers that during one of their escapades, Jack ended up saving his life when the three of them were wandering the world. He admits to Jack he hasn't seen Mike in four years, and Jack comments that she was always hot for MacGyver. Jack claims that he hasn't seen Mike in a long time… but MacGyver can't see that Jack's left eye is twitching.
They arrive in Dinato the next morning and Jack claims that no one should have even noticed he was gone. The police arrive at the airfield and give chase. While Jack tries to buy enough time to get speed for takeoff, MacGyver tapes two baling hooks to an oxygen tank and fires it at pursuing vehicles with a makeshift catapult. The tank explodes, taking out one jeep and giving them enough time to get airborne. The police captain, Antunnez, watches them go. His accomplice, a civilian named Sonny, complains that Jack has their money. Antunnez assures him that Jack won't leave without the girl.
Jack lands at a hidden airfield at an airplane junkyard in the jungle. They discover that a stray shot hit the fuel tank, costing them much of their fuel before MacGyver plugs the leak. Jack has the orchids inside an abandoned airplane and finally explains that Antunnez and his drug-smuggling partner Sonny tricked Jack into smuggling heroin out with the orchids. When Jack learned what was going on, he tried to leave and the criminals grabbed the botanist. Realizing that Jack is now talking about a single botanist, MacGyver asks who it is and Jack "remembers" that it's their friend Mike.
Antunnez and Sonny are holding Mike at the monastery they're using as a base of operations. When she finally convinces them she doesn't know where Jack is, Antunnez prepares to eliminate her but Sonny says they should keep her as a hostage.
Jack tells MacGyver that he has a plan to rescue Mike. They go into town and talk to Elena, the owner of a local cantina who brokers information. They start to talk with Elena, but Antunnez and his men spot them. MacGyver holds them off by pouring beer on a string of lights and setting them on fire, and he and Jack split up. MacGyver hides in a doorway but watches in horror as Jack surrenders to the police.
MacGyver convinces Elena to take him to the monastery where Antunnez is holding the prisoners. Elena warns that the monastery is impenetrable, but that Antunnez let the monks hold a funeral a few weeks ago. Meanwhile, Sonny gives Mike and Jack a day to return the heroin or he'll kill them both. Once he's gone, Jack assures Mike that MacGyver will rescue them, all according to Jack's plan.
The monks bring a wagon with coffin into the monastery. A suspicious Antunnez confirms the identity of the monks and then has them unload the coffin on the ground. He shoots it with a rifle and then tells them to be on the way. While he's distracted, MacGyver slips out of a hidden compartment in the wagon and goes inside. Dressed as a monk, MacGyver slips in to the monastery and knocks out the guard. He frees Jack and Mike and they get outside. Working together, MacGyver and Mike hotwire a truck and escape, driving past Antunnez and Sonny. Sonny is worried they'll make good their escape out of the country but Antunnez assures him he knows where Jack's plane is hidden.
Once the truck runs out of gas, the trio starts walking. Jack starts to weaken from the strain and briefly collapses. They get to the hidden airfield only to discover that Antunnez's men have secured Jack's plane. Jack admits they didn't have enough fuel to escape anyway, but at least he'll die with his friend. MacGyver tells Jack to surrender to Antunnez and buy them a half-hour so that they can get to the hidden heroin and set up a trade. At the abandoned airplane, MacGyver rigs a battery and a prop to create a net trap. As they conceal the trap, MacGyver gives Mike one of the orchids. They kiss and he admits it's good to see her.
Jack surrenders to Antunnez and offers a deal. He takes Antunnez and Sonny to the airplane and MacGyver emerges from hiding to offer them the heroin for Jack's plane. MacGyver leads Antunnez and Sonny to the plane and sets off the trap. It snags Sonny but Antunnez leaps clear. He prepares to shoot them all but Jack offers him a new deal: he'll sign on as Antunnez's pilot to smuggle the heroin. The corrupt police captain can't afford to kill three Americans and brings the U.S. government down on his head. MacGyver objects but Antunnez agrees and tells Jack to tie up MacGyver and Mike. As he does so, Jack slips MacGyver his Swiss Army knife and assures them that this way he'll be dying for a noble cause. He leaves with Antunnez and the drugs. MacGyver cuts himself and Mike free but too late to stop Jack from lifting off with Antunnez.
Later, back in the States, Mike wonders why Jack never told her he was dying. MacGyver figures Jack just wanted to have fun and didn't want to ruin it for her. Pete checks with the Colombian Navy and learns that Antunnez saw Jack's engines start smoking and leaped out into the ocean. MacGyver remembers that Jack had his engines rigged and explains to Mike that Jack might have stretched the truth about how much fuel he had.