At a solvent company, a fire breaks out. As the fire department responds, more fires break out across town. Later, the arsonist plants an incendiary device in an abandoned building.
MacGyver is working at home when Mama Lorraine comes to visit him with fresh food. He explains that he's reconstructing a firebomb for the arson squad. They're investigating the fires, all caused by a bomber calling himself Prometheus who thinks he's purifying the world. MacGyver borrows some of her flash powder to test his reconstruction.
Prometheus finishes his bomb and seals it up, and sets the 4-minute timer.
Arson squad investigator Earl Stringer is trying to work out the pattern behind Prometheus' attacks. His coworker, Rachel Bradley, insists they need a psychiatric work up. However, Stringer figures Prometheus is a professional and they need to use detective work to figure out what he's using. Rachel dismisses him as a dinosaur. Joe Roswell comes in and admits that the fingerprint report is a dead-end. MacGyver arrives with the reconstruction and explains that it has a single on-off toggle switch and a motion detector to set it off as necessary. MacGyver demonstrates with the flash powder and the bomb goes off on time. Rachel points out that it doesn't prove anything and Prometheus is using something hotter than thermite, that burns in the nine to ten thousand degree range. At that heat, there's little or no evidence left. Earl gets a call from Prometheus on the emergency line. The arsonist places his pre-recorded call through a phone booth and says that he'll destroy every sinkhole in the city if he needs to. He tells them to go to a hotel and watch his vengeance. The team takes off and brings MacGyver along with them.
The arson squad arrives at the building and Earl has Roswell take photos of the crowd. The fire department finds a bomb with a four-minute timer, and the bomb squad won't get there in time. MacGyver and Earl go in to defuse the bomb. They have two minutes left and MacGyver manages to open the case while Earl takes photos. It contains thermite but something else to make it burn hotter. MacGyver notices an insulated hand grip wired into the case as he disarms the motion detector. He then realizes that there are two toggle switches, but the one he reconstructed only has one. He throws one of the switches and the bomb shuts off with three seconds to spare. However, a secondary trigger goes off and they run out the door. Earl is last out the door and dies in the blast.
As MacGyver gets treatment, Roswell tells him that Rachel now assumes Earl's command. Rachel comes over and reveals that kids found the tape player that Prometheus used. She orders Roswell to begin compiling a psychiatric profile despite his objections and speculates that a fire may have burned Prometheus. MacGyver and Roswell go over Earl's photo and realize that the handgrip functioned as an antenna. Rachel calls Roswell over and tells MacGyver that she's taking him off the case. MacGyver insists that Earl was a friend and he can't walk away, but she insists he's a civilian and doesn't want to be responsible for his life. Rachel blames MacGyver for Earl's death, insisting she would have waited for the bomb squad if she'd been in charge. Once she leaves, MacGyver wonders why Prometheus broke his pattern and called in an emergency before the bomb went off. He figures Prometheus needed a clear sight line to set off the bomb when he knew they were there, and that he must have been on a rooftop.
MacGyver surveys the nearby buildings and goes over to a hotel that has a third floor with a line of sight. The manager takes him up and explains that junkies come in there and he can't show the place. MacGyver goes out on the fire escape and determines it has a clear sight to the room where the firebomb was hidden. Rachel is there and sees him watching her.
MacGyver attends Earl's funeral and talks to his wife Betty. He asks if Earl brought his work home and she says that one fire in particular bothered him, a cafe fire from two years ago. She heard him on the phone talking to someone about the insurance at the cafe and Earl said a woman was the common denominator. MacGyver asks her about Rachel and Betty explains that she was originally friends with Earl, but Earl got the promotions. When Earl took command of the arson squad, they disagreed about a procedure on a fire and Rachel's hands were burned as a result. As MacGyver leaves, he notices Rachel watching him from the across the street in her car.
MacGyver goes back to the arson squad and notices the hotel manager driving away. Rachel is receiving her promotion as MacGyver enters the office. She tells him that he's off the investigation but MacGyver asks her if the manager came there to see him. Rachel admits that he did and admits she went to the Stringer house to find out if Earl told Betty anything. MacGyver bargains for info and Rachel explains that the manager remembered a man who hung around the hotel with a woman who rented the apartment. However, the manager doesn't remember the man. In exchange, MacGyver tells Rachel that Earl thought was a woman was the common denominator, and she was involved with the cafe fire. Rachel explains that her hands were injured in the cafe fire when Earl attempted an unorthodox rescue attempt. She insists she doesn't want her pity and says she'll check out the woman if she thinks she's worth it.
MacGyver checks the files and discovers that the woman, Victoria Arnold, owned the cafe and died in the fire. Roswell visits him to confirm that koldexin was used to enhance the effects of the thermite. It's also used in the processing of pesticides, petroleum products, and newspaper color photography. MacGyver thanks Roswell for his help and Roswell insists Earl would have done the same thing.
MacGyver goes back to the hotel to talk with the manager and see if he remembers the man who lived with Victoria. The manager says he told Rachel that the boyfriend worked at a newspaper but it went out of business. He promises to tell MacGyver anything else he remembers. Before he goes, MacGyver writes down the address of the hotel. He goes to the newspaper and a guard lets him look through the files. MacGyver goes through the files trying to find an employee who lived at Thatcher. He finds the name of a Ralph Boardman, a color plate engineer. They go to Boardman's desk at the color lab, unaware that Prometheus is watching from the shadows.
The guard leaves MacGyver with the files. He discovers files showing that Boardman worked in the Army as a demolition expert. MacGyver finds Boardman's desk and an envelope labeled "Victoria". Prometheus calls out to him using a voice synthesizer and leads him up the stairs. As MacGyver follows, Prometheus taunts with him with Earl's death and boasts that he'll always be one step ahead of everyone. MacGyver follows him into a paper storeroom and discovers another firebomb. Prometheus slips out behind him and locks the door, and then warns him about the motion detector and other surprises that he's planted.
Using an ink pen refill cartridge, MacGyver gets the bomb open and deactivates the motion switch. He throws the toggle switch but a magnetic circuit cuts in when the power is cut, reactivating the bomb. Thinking quickly, MacGyver brings over an electric forklift cart and runs a fork through the bomb's handle. He then uses a slat to jam the forklift switch and let it carry the bomb into the door, blasting it open. MacGyver covers himself with a cloth and runs out through the flames. The guard comes to investigate and MacGyver tells him to call it in and then goes back to Boardman's desk. The envelope contains photos of the cafe fire and show Earl and Rachel. MacGyver takes the photo with him and goes outside where Roswell arrives with the fire department. MacGyver confirms that Rachel is at the office and drives there to see her.
MacGyver runs into Rachel's office to tell her who Prometheus is, but discovers she's been tied and gagged and a firebomb placed in her lap. He removes the gag and realizes that the firebomb hasn't been activated yet. Prometheus comes in and reveals that he's the hotel manager. He forces MacGyver to handcuff himself to Rachel's chair while Boardman explains that his clues were supposed to lead Rachel to the newspaper office. Boardman says that he wants revenge on everyone he holds responsible for Victoria's death. MacGyver tells Boardman that he and Victoria started the fire for the insurance, and Earl almost figured it out. Boardman insists that he died and is now Prometheus. He triggers the firebomb with a remote control and runs out to watch from the street. MacGyver uses the pin from Rachel's badge to push out the hinge pin and then deactivate the motion sensor. He prepares to throw the switch but wonders if Boardman anticipated him. He throws the switch the same way, triggering the magnetic circuit. Finally, MacGyver uses the magnetic plate from a walkie-talkie to reverse the polarity and stop the bomb. Rachel goes to the window and distracts Boardman while MacGyver comes up from behind and knocks him out.
As Boardman is taken away, MacGyver shows Rachel the photo of her and Earl at the cafe fire. Boardman was in the background. Rachel insists that she'd turn in her badge if it would bring back Earl and MacGyver admits he knows that about her.