MacGyver has set up a wilderness training course to recertify Phoenix Foundation agents for field operations. His last subject breaks his leg and has to be flown out. Pete arrives and MacGyver complains that he doesn't feel right judging his peers. Pete tells him he has one more person to test: Pete. He admits that he's been trying to avoid recertification as long as possible but is determined to continue working as a field operative.
The next day, MacGyver and Pete rappel down from a helicopter and go to MacGyver's obstacle course. MacGyver demonstrates the course with ease but Pete falls down halfway through. As they camp for the night, Pete is initially hostile, accusing MacGyver of patronizing him. Finally he admits that he's worried he'll flunk and made sure that MacGyver would test him so that if he did fail, it'd be at the hands of a friend. Pete wonders what it'd be like to retire and MacGyver reminds him that the last time he retired, he was bouncing off the walls after two days. Pete is determined to continue.
The friends forage for food and find the wreckage of a small plane. Investigating, they discover that the two dead pilots are DEA agents who were conducting aerial surveillance. Someone shot at the plane with a missile launcher and brought it down. The plane radio is dead and civilization is three days away. MacGyver uses chemicals from their first aid kit to develop the film long enough to determine who shot down the DEA plane. The footage reveals that two men with a missile launcher were landing a seaplane at Crystal Lake, six hours away. Pete has no choice but to accompany MacGyver to the lake and use the seaplane's radio.
As MacGyver and Pete get to the lake, the two smugglers, Wilcox and Crandell, fly in from the ocean and land on the lake. Wilcox, the pilot, is worried that someone will notice the DEA plane's absence. However, Crandell warns him that if they don't make their delivery, their buyers will kill them. They only have two more runs to make, moving the drugs from the lake to the ship out at sea.
Once the smugglers leave, MacGyver and Pete search the area and find a generator. The cables lead to a cave containing weapons, supplies, and millions in cocaine. They break open a crate and take a bag of cocaine for evidence, but the smugglers return and Pete and MacGyver are forced to hide in a side passage. When the smugglers come in, Wilcox spots the opened crate and calls out to Crandell. Crandell spots Pete's stomach sticking out and moves in, and MacGyver throws the cocaine in his face. MacGyver and Pete run down the tunnel and come to a cavern with no way out. Crandell tosses a grenade into the cavern. MacGyver manages to throw it far enough out to survive the explosion, but the blast brings down the tunnel.
MacGyver looks for a way out and spots a hole in the roof. The only way to get there is a perilous ascent. MacGyver puts together a grappling hook out of a climbing hammer and a rope and he and Pete slowly ascend up a series of ledges. At the last ledge Pete almost falls but MacGyver uses some roots to pull him to safety.
MacGyver hooks his makeshift grappling hook on the edge of the hole but the noise attracts Wilcox's attention. He goes to investigate and MacGyver is forced to toss the hammer and rope down to Pete, who misses it. Wilcox gives up and goes back to the seaplane, and MacGyver helps Pete climb out.
MacGyver borrows Pete's coat, stuffs it with branches, and then runs through the woods near the smugglers. They spot the dummy and figure it's Pete and MacGyver and give chase. Once they're gone, Pete sneaks out of the woods and calls the Phoenix outpost on the seaplane radio. Meanwhile, MacGyver loses his grip on the dummy and the smugglers catch up to it. Realizing they've been tricked, Crandell goes back to the seaplane while Wilcox pursues MacGyver. MacGyver ambushes the pilot and knocks him out.
Crandell returns to the seaplane and shoot Pete. Bleeding from the head, Pete falls into the water and goes under. MacGyver hears the gunshot and comes back, and Crandell gets the drop on him. However, Pete, only grazed, rises out of the water and trips Crandell, and then punches him unconscious. MacGyver is happy to inform his friend that he's passed.
Later at the Phoenix outpost, the smugglers are taken away and a battered and bruised Pete recuperates in a bunk. He thanks MacGyver for recertifying and MacGyver admits he's always looked up to Pete.