In Mongolia, MacGyver is scaling a mountain and approaches a plateau where a USAF fighter has crashed with a top-secret missile. Soldiers have set up camp and taken the pilot prisoner. MacGyver knocks out a guard at a machine-gun post, takes his uniform, and slips past the guards to the plane. He takes a flare gun out of the cockpit and puts it in his bag, then spots a survivor, the pilot. MacGyver finds out from him which tent the missile is in and slips the man his Swiss Army Knife to cut himself free. MacGyver slips under the edge of the tent and uses a set of specialized tools to start disarming it. He removes the main circuit but sets off a 30-second timer. With seconds remaining, MacGyver uses a paper clip to stop the countdown. He then rigs a rifle to fire into the ground and heads for the pilot, who has cut himself free. The gunshots attract the guards and the pilot gets out, while MacGyver knocks out a guard. They head for the edge of the cliff as the guards open fire. MacGyver opens fire to hold them off and gives the rifle to the pilot, then takes out a parachute from his backpack. He dons it and grabs the pilot, then flattens the barrel of the flare gun, grabs the pilot, and fires the flare gun. The blast shoves them far enough off the cliff to get clear and make a safe drop.
Back in the States, MacGyver has a Little Brother in to visit the observatory where he lives. Meanwhile, in Bannon, New Mexico, British scientist Dr. Marlowe arrives at a classified desert laboratory facility dedicated to studying the ozone level. Dr. Barbara Spencer greets him on behalf of Dr. Steubens, who has been delayed on the third level. She takes Marlowe 300' down by elevator after he passes through a security scanner. Steubens greets Marlowe and invites him to take the next move in their correspondence chess game. Spencer returns to the upper levels, and they play out their game, unaware that a bomb is hidden nearby. Precisely at 11 a.m., the bomb goes off, devastating level 3 and rupturing a tank filled with sulfuric acid.
Ed Gantner arrives at the observatory to brief MacGyver on a mission: Steubens and Marlowe, Nobel Prize nominees, are trapped and it's not known if they're alive or dead. MacGyver is their only chance. MacGyver agrees to accept the mission.
In the lab's control room, the technicians briefly get through to Dr. Marlowe, who warns that Steubens is injured but coming around. MacGyver and Gantner arrive and talk to the head technician, Charlie Burke. MacGyver wonders what set off the explosion but Burke insists that it must have been an accident given their security measures. Burke warns they only have ten hours before the air runs out. Worse, the acid is leaking into the aquifer that feeds into the Rio Grande. They have to flood the compound with sodium hydroxide, which will kill Steubens and Marlowe, and they only have just under five hours. They pinpoint the lab on the map and MacGyver talks with Andy Colson, their chief of operations. MacGyver plans to take a two-way with him and the only way down is through the elevator shaft, which is rigged with lasers. MacGyver borrows one of Colson's cigarette, and Colson warns he won't be able to see the lasers.
MacGyver takes a two-way radio and heads down the access tunnel to the elevator shaft. He kicks off the grille, which sets off the lasers. MacGyver lights up Colson's cigarettes from the laser and uses the smoke to spot the laser beams. He then uses a binocular lens to bounce one of the lasers back on its projector, destroying it. He climbs down and enters the elevator shaft, and then starts his descent to level 3. The corridor is caved in ahead and he hears a tapping noise. He climbs up into a gap in the wreckage to find his way blocked by a girder. Using a discarded woman's shoe, he signals back. He then takes a fire hose and runs it under the girder, He turns on the water and the pressure raise the girder enough for him to swing it loose. He falls into the lab on the other side and discovers the surviving laboratory staff. He sends them back to the elevator shaft but Spencer overhears MacGyver talking to Colson and says she can take him there. MacGyver is reluctant but she insists on going to help Steubens.
They descend down a ladder and MacGyver asks if she knew what set the blast off. She admits she doesn't but he notes the explosions are tied into the labs. They come to a door and MacGyver notices smoke rising up. He tests the doors and discovers they're red hot. With three hours, twenty minutes left, Spencer tells him there's a series of airlocks they can use to bypass the heated area. As they head down the hallway, MacGyver picks up some chocolate candy bars spilled out of a vending machine. They come to the airlocks and they start to close as the emergency alerts activate. They manage to get through just ahead of the doors and get to the central laboratory, only to discover that it's filled with poison gas.
Marlowe tends to the injured Steubens, while above the tankers arrive and they prepare to flood the complex in 50 minutes.
Colson and his team work to open the airlocks but the controls short out. The airlock controls are on the other side of the lab and Spencer points out the panel they need to get to. MacGyver makes up some crude gas masks out of his shirt and Spencer kisses him in thanks. He breaks open the window and they head through the lab to the control panel and activate the pumps to remove the gas. MacGyver and Spencer escapes through a hatch, while up above Gantner learns that the government is going to fuse the rock between the lab and the aquifer by firing a missile to seal it off. With thirty-one minutes remaining, Gantner tries to warn MacGyver... who has dropped the radio.
Spencer leads MacGyver to the acid tank. He has her get up on his shoulders and stick the chocolate bars into the rupture: the chocolate will react with the acid and cause a resin to seal the leak. With nine minutes remaining, they seal the link and make their way to a metallurgy lab next to Steuben's laboratory. The door is blocked and Spencer reaches Marlowe via the intercom. MacGyver examines the rubble and determines that plastique was the source of the explosion. MacGyver warns the scientists to take cover and then goes through the laboratory trying to find an explosive. He finds sodium and then borrows a cold capsule from Spencer. He carefully puts the sodium in the cold capsule, then puts the cold capsule in a glass jar filled with water. MacGyver places the jar next to the rubble: the cold capsule dissolves and the sodium explodes on contact with the water. As they wait, MacGyver tells Spencer to let him go in first while she waits outside.
With four minutes remaining, the makeshift bomb goes off and MacGyver enters Steubens' laboratory. Steubens pulls out a gun and Spencer comes in. Steubens explains that he planted the bomb and Marlowe wasn't supposed to survive. The government planned to use Steubens' research to make the ozone level self-destruct, so he called in Marlowe, the only other expert, to destroy them both. Spencer rushes Steubens and the gun goes off, shooting her in the stomach. MacGyver disarms Steubens and tends to Spencer, who mentions power. MacGyver goes to the power generators and turns the power on and off in Morse code to signal that they're alive and have sealed off the acid. With seconds remaining, they abort the launch.
Later, Spencer is taken out and MacGyver gives her one last kiss despite her cold. Back at the observatory, MacGyver meets with his Little Brother to play some basketball.