MacGyver is conducting survival training for Phoenix Foundation agents. MacGyver is less than thrilled at the duty, being put in the position of judging his peers. Pete arrives at the Foundation's training outpost and MacGyver admits he doesn't like having to flunk one of his students, who broke his leg. It turns out that Pete has one more student for MacGyver: himself. He's been dodging it as long as possible but insists that he has to go through the same test as everyone else. MacGyver figures that he's worried and Pete has to agree.
The next day Pete and MacGyver rappel down from a helicopter into the wilderness and MacGyver's personally prepared obstacle course. MacGyver demonstrates but has to admit that's where his previous student broke his leg. Pete slowly makes his way through the course and finally falls to the ground. They proceed and that night settle in. Pete worries that he's washing out and refuses to be patronized, but then admits he wanted to have MacGyver review his performance so if he washed out, it'd be with a friend. Pete wonders if he'd have to retire but MacGyver warns that he'd go nuts after two days. Pete, inspired, decides to continue on.
As they forage for food, MacGyver spots the tip of a small plane wing on the ground. They follow the debris to a plane where two men are dead, having crashed within the last 12 hours. Pete spots a camera mounting and the IDs show that they’re DEA agents conducting aerial surveillance. The engine has been shot away with a missile launcher and the radio is dead. Pete insists they have to alert the authorities but MacGyver warns it's a three-day trek. MacGyver improvises the chemicals necessary to develop the film from the camera for the few seconds they need. They discover the DEA plane was flying over a lake with a seaplane, and two men holding a missile launcher. Pete figures it's a heavy drug operation and the only lake large enough to support a plane is six hours away. Pete has no choice but to go along as they go to get to the seaplane and radio for help. He insists he won't slow MacGyver down.
The two men make their way through the woods and Pete starts to lag behind. As they approach the lake, they notice the seaplane fly overhead from the ocean toward the lake. The seaplane lands and the two criminals, Wilcox and Crandell, anchor the seaplane. The pilot, Wilcox, worries that someone will come looking for the DEA plane and they should head out, but Crandell warns that their buyers will kill them if they don't get their drugs and they have two more runs.
Pete and MacGyver get to the lake and see the crooks depart on their next run. They head around the lake to check out the mooring spot while at sea, Wilcox and Crandell make their next pickup. MacGyver and Pete search for the smugglers' cave and find a generator. They trace the power cable to a cave and find the smugglers' supplies and bags of cocaine. The seaplane lands outside as they take a bag for evidence. MacGyver hears the plane and they head for the cave entrance. The smugglers get in sight of it first and the two men retreat into the cave and hide in a side passage. Crandell turns on the generator and Wilson goes inside. He spots the opened bag of cocaine and calls Crandell in. Crandell spots Pete's stomach sticking out and calls for Wilcox. MacGyver throws the cocaine in Crandell's face and he and Pete run down the passage. They come to a dead-end cavern, while Crandell grabs a grenade and tosses it in. MacGyver tosses it far enough out of the cavern to avoid the blast, but the explosion brings down the entry tunnel.
As the two friends recover, they spot a hole high up on the ceiling. MacGyver makes a grappling hook out of a hammer and he and Pete start to ascend. They climb partway up and then MacGyver uses the grappling hook to attach a rope to the neighboring wall. He anchors it and then climbs across, Pete eventually managing to follow. MacGyver hooks the rope to the last ledge and swings across. Pete tries to make it and fails. He dangles from the roof of the cavern and MacGyver manages to toss him some roots and pull him to safety.
MacGyver tosses the hammer up and hooks it, but the noises attracts the smugglers' attention and Wilcox goes to investigate. MacGyver climbs up first and spots Wilcox. He throws the hammer and rope down to Pete, who misses it. Wilcox gets closer but spots nothing and Crandell calls him back to the seaplane before he can spot MacGyver. It's too far for MacGyver to reach Pete, who has to climb. He manages to get out and MacGyver comes up with a plan. He'll draw Wilcox and Crandell away from the plane while Pete gets to the seaplane and uses the radio to call for help.
A few minutes later, MacGyver goes near the seaplane, carrying Pete's coat stuffed with branches. He runs away and the smugglers figure both Pete and MacGyver are escaping. They chase after MacGyver while Pete gets to the seaplane and calls the outpost for help. MacGyver trips when he snags the coat on a branch. Wilcox and Crandell realize they've been fooled and Crandell goes back to the plane. MacGyver leaves his coat on the floor to lure in Wilcox and then ambushes him. Crandell returns just as Pete leaves the plane. He shoots Peter, hitting him in the head and knocking him into the water. MacGyver hears the gunshot and comes running while Crandell checks the water. He spots MacGyver coming and hides in the seaplane, and them ambushes him when he gets close. As Crandell prepares to shoot, Pete, only grazed, comes out of the water, knocks Crandell down, and knocks him unconscious. MacGyver pulls him off Crandell and assures him he's passed.
Later, the smugglers are taken back to the outpost and hauled away by the police. The nurse takes care of Pete and MacGyver asks what he can do for his friend. Pete thanks MacGyver for his help in recertifying as a field agent and MacGyver admits he's look up to Pete all the years they've known each other.