In Central Asia, MacGyver scales a sheer cliffside to a plateau where enemy soldiers have recovered a USAF fighter that has crashed with a fied missile. MacGyver sneaks up on a guard, knocks him out, and takes his uniform. As he passes by the fighter, he take a flare gun out of the cockpit. He then enters the camp and discovers that the pilot is still alive and a prisoner. MacGyver throws him his Swiss Army Knife to cut himself free then sneaks into the tent where the missile is kept. MacGyver starts to disarm it but a 30-second timer goes off. When MacGyver's pack of bomb disarmament tools prove insufficient, he uses a paper clip to stop the timer and remove the main circuit.
Slipping out of the tent, MacGyver rigs a branch to fire a rifle and uses a book of matches as a makeshift timed delay. He gets to the pilot as the rifle goes off, drawing the soldiers' attention. MacGyver and the pilot head for the cliff side. The soldiers corner them and while the pilot holds them off, MacGyver uses a rock to narrow the barrel of the flare gun, and then dons a parachute. He grabs the pilot and fires the flare gun, which acts as a makeshift rocket to propel them far enough away from the cliff face so they use the parachute to make their escape.
Back in the States, MacGyver is at his home at the Griffith Observatory and entertaining his Little Brother, Reggie. Meanwhile, Dr. Sidney Marlow arrives at a fied laboratory in the desert outside of Bannon, New Mexico. Dr. Barbara Spencer greets him and escorts him through the security scans and down to Level 3, 300 feet underground. The head scientist, Dr. Carl Steubens, is waiting for Marlow, having invited him there to inspect his work and finish their correspondence game of chess. Barbara leaves them to their game… unaware that someone has planted a bomb in the Level 3 laboratory, set to explode at 11 a.m. At 11, Steubens wins the game and apologies to Marlow as the bomb explodes, devastating the facility and rupturing a tank of sulfuric acid.
Ed Gantner arrives at the observatory to tell MacGyver that they need his help. Steubens and Marlow are trapped and the government needs MacGyver to bring the valuable scientists out alive. MacGyver agrees and they head to the surface control room of the laboratory. The head technician, Dr. Charlie Burke, briefs them on the situation and informs them the explosion must have been an accident. Burke warns them that there's only ten hours of air left and the sulfuric acid is leaking into the aquifer. In five hours it will leak into the Rio Grande, contaminating the water supply of half the state. They will have to flood the complex with hydrogen peroxide to negate the acid… and the chemical will strip the flesh from anyone inside. The Head of Operations, Andy Colson, shows MacGyver a map of the facility and says the only way down is through the elevator shaft. However, the elevator shaft is protected with lasers. MacGyver takes a two-way radio headset and borrows a pack of cigarettes from Colson, who warns him the lasers are invisible to the naked eye.
MacGyver takes a ventilation tunnel to the elevator shaft and kicks out the grille, triggering the lasers. MacGyver lights the pack of cigarettes on a laser and uses the resulting smoke to see the beams. He then breaks open his binoculars and uses the lens to reflect a laser beam into the projector, burning it out. He goes down the shaft and enters the car on Level 2. The shaft is blocked and MacGyver heads through the passageways looking for another way down. He finds a cave-in and hears tapping on the other side. A girder blocks the way and MacGyver uses a fire hose as a crude hydraulic pump, wedging it beneath the girder and turning the water on. Once it sufficiently rises, MacGyver shoves it aside and falls through to the other side, where the Level 2 survivors have gathered. He sends them back to the elevator shaft but Barbara is there and offers her help in getting MacGyver to Level 3. He's reluctant to risk her life but she convinces him to take her with him.
As they descend down a shaft, MacGyver admits he doesn't believe that the explosion was an accident. He notes that the explosion was tied in with all the laboratories. They find a door but it's emitting heat from the room beyond. They need an alternate route and Barbara directs MacGyver to a series of airlocks that will get them around the heated area. As they proceed down the hallway, MacGyver spots a broken vending machine and takes some chocolate bars. As they pass through the airlocks, the emergency circuit kicks in and they manages to get through the area just ahead of the last door closing. They're trapped above a laboratory, and Barbara realizes that the room has filled with poison gas, killing everyone inside and making the room impassable.
While Marlow tries to bandage Steubens, tankers arrive with hydrogen peroxide. In 50 minutes they'll flood the compound.
Colson and his technicians can't override the airlock doors. The only way to get through is to pump out the gas. MacGyver fashions crude gas masks from his shirt and breaks the window leading into the laboratory. He works the controls and manages to pump the gas out, and he and Barbara escape through the hatch. On the surface, Gantner learns that the Army plans to fire a missile to seal off the laboratory from the aquifer in 31 minutes. The missile will destroy the facility and everyone inside. Gantner tries to warn MacGyver… who has dropped his two-way radio.
Spencer finds the acid tank and he explains that they can use the chocolate bars to create a resin to seal the leak. She gets up on his shoulders and sticks the candy bars into the leak, and the chocolate reacts with the acid to create the resin.
With nine minutes remaining, Barbara and MacGyver get to the metallurgy lab next to Steubens' laboratory. Barbara contacts Marlow over the intercom while MacGyver examines the rubble and finds traces of plastique, meaning the explosion was no accident. MacGyver tells Marlow and Steubens to take cover and then finds a canister of sodium. He borrows a cold capsule from Barbara, puts the sodium into it, then puts the capsule into a jar of water. He puts the jar against the adjoining wall and head for cover, and the cold capsule dissolves. The water sets off the sodium, causing an explosion that blasts open the wall. MacGyver tells Barbara to stay behind while he goes in first.
Inside the lab, Steubens pulls a gun and explains that he planted the bomb and invited Marlow. Steubens has discovered an ozone-destroying technique that he feared the government would use as a weapon. Only he and Marlow understand the technique, so Steubens planned to kill himself and his friend so the secret would never be revealed. Barbara comes in despite MacGyver's orders and rushes Steubens. The gun goes off and she's wounded. MacGyver disarms Steubens and checks on Barbara. With only a couple of minutes remaining, Barbara notes that they have no way to communicate to the people above. MacGyver gets an idea and goes to the power plant, then turns cuts the power on and off in a Morse code sequence. On the surface, a technician recognizes the Morse code and deciphers it. They realize that the acid has been neutralized and stop the missile launch just in time.
Later, Barbara is taken out on a stretcher and MacGyver gives her a kiss, then heads back to his home for a little one-on-one basketball with Reggie.