MacGyver and Pete are returning from a ski weekend that didn't go exactly as planned. Pete started a fight with the resort owner after he was cut off, and they were kicked out for life. The gar runs out of gas and Pete admits he forgot to fill it up. They split up and go to find a gas station.
Down the road, three Black Dove Front terrorists kill the owner of a gas station, and their leader, Jonathan, spots MacGyver. He puts on the owner's jacket and goes out to make conversation, pretending to be the owner. As MacGyver fills up a gas can and explains he and Pete split up, he drops his wallet and Jonathan spots his Phoenix Foundation ID. He lets MacGyver go and the other two terrorists, Lisa and Armin, wonder why. Jonathan explains that they may have use of a Phoenix employee later and then calls their fourth teammate, Frank. Frank is at a cabin working on an electronic device. Jonathan tells him to capture Pete. Frank drives down the road, picks up Pete, and forces him into his vehicle at gunpoint.
Two drivers transporting a large generator-like device pull up to the gas station for a meal. Lisa poses as a waitress and gets close enough to gun them down. Meanwhile, Frank takes Pete back to the terrorists' cabin and locks him in the cellar. Jonathan and the others set up the generator device off the road and Frank meets with them to examine the device. He has Armin hook it up to a nearby transformer and shows Jonathan how it can generate an EMP wave capable of shutting down electrical devices. When MacGyver drives by looking for Pete, they activate the device and the jeep shuts down. The terrorists take him prisoner and transport him to the cabin where they lock him up with Pete. Jonathan boasts that the four terrorists plan to take over an entire city and prove how impotent the U.S. military is. He plans to keep MacGyver and Pete alive so they can testify that the Black Dove Front was responsible for the chaos. Jonathan ties them up with their hands behind their backs and then has them hold grenades with the pins removed. As he leaves, Jonathan assures them that he'll tell the authorities their location once the operation is a success.
Jonathan goes over the blueprints of their two targets: a transmission station and a telephone exchange. He figures that the military will cover up their success, but that Pete and MacGyver will tell the American people what happened. The terrorists split up and leave for their targets. In the cellar, Pete tries to come up with a plan. If they use the grenades on the door, the entire cabin will collapse on them. Pete suggests they use something to replace the pins and MacGyver starts to come up with a plan.
Jonathan and Frank gain access to the unguarded transmission station and hook up a VCR to the broadcast equipment. Armin and Lisa destroy the telephone exchange, cutting off communication in and out of the area. At the cabin, MacGyver places his grenade under Pete's chin and then uses the ski ticket wire as a makeshift pin. He then frees himself and his friend and removes the C4 detonator from one of the grenades. Using the grenade pull-handle as a makeshift trigger device, MacGyver attaches the charge to the cellar door and then uses string to activate it from a safe distance. Once free, they realize there's no phone so they hotwire Frank's truck and drive to the gas station to call the authorities. They get there and discover all the phones are dead, then locate the dead drivers. Upon finding a company ID, they realize that the drivers were transporting a piece of electro-magnetic equipment. Jonathan's transmission begins and he announces that the government must release their leader, and if they fail to do so they will attack a major city and shut off all electrical power. Jonathan gives the authorities one hour, until 1 p.m., to meet their demands.
Pete and MacGyver go over what they know, and MacGyver realizes his watch stopped at the same time as the jeep. They conclude that the terrorists stole an EMP generator and then created a communications dead zone by knocking out the telephone exchange. They'll need plenty of power to enable to EMP generator to take out an entire city, and realize the only place inside the dead zone with enough juice is a power laboratory.
With 20 minutes until the deadline expires, the terrorists get to the laboratory and take the staff hostage. Frank locates the high-capacity storage magnet but discovers that it's empty. He suggests they hook it up to the regulator to charge it up in time to meet the deadline, but warns that it's a risky procedure. Jonathan tells him to go ahead.
MacGyver and Pete arrive and sneak into the building. They jam the door where the terrorists are holed up and then string a cable across the floor. MacGyver runs for the regulator and Jonathan and Lisa spot him. Pete trips them with the cable once they break through the door but they recover their guns and take him captive. MacGyver climbs up the regulator tower and the terrorists are unable to open fire without damaging it. He gets to the top and tries to break the connection. Jonathan orders Frank to proceed with the charging procedure, despite the fact Armin is still on the battery. The charge goes off as planned and Armin is killed. Lisa tries to shoot Jonathan for killing her partner, and Jonathan kills her first. Jonathan and Frank hold Pete as a hostage and leave.
MacGyver confirms with the head scientist that the EMP has a two-mile radius and the nearest vantage point is at the end of a nearby road. The government has refused to release their leader, so Jonathan and Frank continue with their plan. They tie Pete up to a tree and prepare to activate the generator. MacGyver sneaks up and rigs two walkie talkies so that he can use one to short-circuit the other. Franks put the EMP generator on a three-minute timer and Jonathan adjusts the dish. MacGyver puts the rigged walkie-talkie beneath the trailer and activates it, drawing Frank's attention. MacGyver knocks him out, then goes after Jonathan when he comes to investigate. The two of them slide down a slope to a nearby beach, and MacGyver manages to blind Jonathan with sand long enough to knock him out. Returning to the generator, MacGyver discovers that the controls are locked. He uses metal cable to hook up the generator dish to the battery. He then frees Pete and they get clear as the entire generator short circuits and blows up.
Later, Lt. Chambers from the military arrives to take the terrorists into custody. He plans to cover up the entire thing since the military was financing the generator's development. Pete assures him that the Phoenix Foundation will disclose the entire thing to the public. As Chambers stalks off, MacGyver asks what Pete has planned for next weekend.