MacGyver and Pete are driving back from a ski vacation and Pete insists it wasn't his fault another skier cut him off. The skier was the owner of the resort, and now they've been banned for life. Neither one is happy with the other. The run out of gas because Pete forgot to fill the tank, and MacGyver gets out. They angrily head in opposite directions on the road to find a gas station.
At a nearby gas station, three terrorists of the Black Dove Front dispose of the owner and the leader, Jonathan, looks outside and sees MacGyver approaching. He puts on the owner's jacket and goes outside to check him out. MacGyver explains he ran out of gas and Jonathan gets him gas. As MacGyver pays him, he drops his Phoenix ID and Jonathan recognizes it. Once MacGyver is gone, the other terrorists Armin and Lisa wonder why Jonathan let MacGyver go. Their leader explains that a Phoenix employee could be useful to them, and they have other things to do. Jonathan then calls their fourth member, Frank, who is working at a cabin and busy working on an electronic component. Jonathan tells Frank to intercept Pete. Frank draws a gun on Pete and takes him to the gas station.
Two drivers pull up to the gas station with a bulky generator. Lisa poses as a waitress long enough to put them at ease, then picks up a gun and kills them. Frank takes Pete to the cabin and locks him in the cellar. As MacGyver is walking back to the car, Jonathan and the others drive by him in the hijacked truck. They drive to the cabin and meet Frank, who assures them they can pull power from a nearby transformer to power the generator and shut down MacGyver's vehicle. Frank sets up the device and demonstrates how it can generate an EMP pulse that will shut down any electrical device and can be operated by remote. MacGyver fills up the jeep and drives in Pete's direction. He turns on the radio and drives by the generator, and Frank activates the EMP generator. The jeep's electrical systems shut down and MacGyver coasts to the side of the road. Armin and Lisa take him prisoner and lock him in the cellar with Pete. Jonathan explains that his four people can take over an entire city using the EMP generator. He's going to have Pete and MacGyver help them. He removes the pins from two grenades and puts them in Pete's and MacGyver's tied hands. He promises that he'll notify the authorities once they've pulled off their operation, so that Pete and MacGyver can testify to what he did.
Jonathan goes over a map and coordinates their operations to take over a microwave station and shut down the nearby telephone exchange. When Armin questions the plan, Jonathan informs him that they'll not only free their leader but demonstrate the inferiority of the American military complex. He's sure the military will try to cover it up, but Phoenix will tell people the truth. The terrorists depart in the truck while MacGyver and Pete try to come up with a plan. Pete suggests they throw a grenade at the door, but MacGyver warns the cabin will cave in on them. Next, Pete suggests they find something to replace the pins.
Jonathan and Frank arrive at the microwave station and shoot open the lock. The guard only checks in twice a day, so they can easily patch in to the broadcast facilities. Lisa and Armin easily gain access to the telephone exchange and destroy it. Back at the cabin, MacGyver puts his grenade under Pete's chin, then takes his ski lift ticket and uses the wire fastener as a pin for the grenade. He manages to insert it just as Pete drops it, and the grenade drops harmlessly to the floor. Once MacGyver cuts his ropes, he frees Pete and removes the C4 detonator from the grenade. He then makes a makeshift trigger device, tapes the shaped charge to the cellar door, and blows open the entrance. There's no phone so MacGyver hot wires the terrorists' truck and they drive to find a phone.
As the terrorists link back up, MacGyver and Pete drive to the gas station but discover that the outside phone is dead. They go inside and find the dead drivers. They figure that the terrorists took out the switching station, and discover the drivers work for a company specializing in electromagnetic technology. Jonathan's pre-recorded videotape starts transmitting from the broadcast station and he makes his demands for the government to release their leader. He warns that they will attack a major city and disable all electronic systems if his demands aren't met, and gives them until 1 o'clock.
MacGyver and Pete have 55 minutes until Jonathan makes good on his threat. MacGyver remembers what happened to the jeep and notices that his watch stopped, and figures that the terrorists hijacked an EMP generator. The terrorists created a dead zone by knocking out the switching station, and will need power for the EMP generator. There's a local high-power laboratory within the dead zone, powerful enough to allow the EMP generator to blanket a city.
As a reporter talks to a scientist who assures the public the terrorists don't have access to the technology, Jonathan and his team arrive at the laboratory and capture the scientists. The terrorists drive the EMP generator in with 20 minutes to spare. Frank finds the high-capacity storage magnet but discovers that it's behind schedule. He warns Jonathan it will take the rest of the day to charge it. Frank suggests they hook it up to the high-voltage regulator but it could blow up the generator. Jonathan orders him to go ahead despite his misgivings.
While the military attempts to reassure the public, Frank and Armin hook up the regulator to the storage magnet. MacGyver and Pete arrive and sneak into the building. They spot Lisa guarding the technicians, confirming their suspicions. MacGyver realizes what the terrorists are doing but there's no way he can pull the plug without being spotted so grabs some cable. He jams the door and then runs a taut cable in front of it. Jonathan and Lisa spot him, knock the door open, and Pete trips them with the cable. They capture him but MacGyver manages to get to the regulator tower and they can't shoot at him without damaging it. Armin completes the hook up and Frank is ready to transfer the charge. Jonathan orders him to do so despite the fact Armin isn't clear. The charge fires into the storage magnet before MacGyver can break the cable, and Armin is electrocuted. Furious, Lisa tries to kill Jonathan, who shoots her dead. Using Pete as a hostage, Jonathan warns MacGyver not to interfere and then leaves in the truck with Frank.
MacGyver talks to the head scientist, who tells him the EMP has a two mile radius and the nearest vantage point is at the end of the road. With five minutes left, the government refuses to negotiate. Jonathan ties Pete to a tree and sets up the EMP generator. MacGyver drives up nearby in the terrorists' van. Going through a tool kit, he finds a pair of walkie-talkies and some cable. Stripping the cable, MacGyver hooks it up inside the walkie-talkie then sneaks up to the generator. Frank finishes powering up the EMP generator and puts it on a three-minute timer while Jonathan focuses the dish. MacGyver places one walkie-talkie on the underside of the trailer, gets clear, then uses the other one to set the first one off. Jonathan believes something has short circuited and sends Frank to investigate. MacGyver knocks him out and Jonathan comes to investigate. MacGyver tackles him and the two men struggle as they roll down a slope. MacGyver throws sand in his eyes and manages to knock him out, then tries to shut down the generator. It's in an automatic sequence so MacGyver runs a cable from the EMP generator dish to the trailer and then back to the battery. With seconds remaining, MacGyver frees Pete and they get clear as the entire thing blows up.
The authorities take Jonathan and Frank away and Lt. Chambers from the Army arrives. He quickly covers up the entire scene but Pete warns that he won't get away with it. MacGyver asks what Pete feels like doing next weekend.