A fire at a solvent company is the most recent in a series of attacks by an unknown arsonist using the name Prometheus. MacGyver is called in by the arson squad to help identify the bomb. Working at his loft, MacGyver tries to reconstruct the bomb. Mama Lorraine comes in to bring him some food, and MacGyver borrows some of her voodoo flash powder to demonstrate the firebomb for the arson squad.
At the squad room, chief investigator Earl Stringer is trying to figure out the pattern behind Prometheus' attacks. His underling, Rachel Bradley, believes that an accurate psychiatric profile of the bomber is the key to success, but Earl overrides her. As MacGyver arrives, their squadmate Joe Roswell reports that the fingerprints are too indistinct to get a match. MacGyver explains that the bomb has an on-off toggle and a motion detector as a secondary detonation device. He demonstrates how the bomb works and suggests that Prometheus used thermite. Rachel notes that the temperatures generated are far hotter then thermite and MacGyver's demonstration is useless. Prometheus calls them for the first time before one of his bombs goes off, and via a pre-recorded message tells them to watch a clothing warehouse across from a hotel.
MacGyver accompanies the arson squad to the clothing warehouse where the fire department has already located the bomb. Roswell takes photos of the crowd in case Prometheus is watching his own work, while MacGyver and Earl go in to examine the fire bomb. It matches the bomb that MacGyver reconstructed but the handle is insulated in wiring. MacGyver uses electrical wiring to push out the hinge pin, and then bends the hinge pin into a pair of tweezers to defuse the motion sensor. He discovers that Prometheus uses two toggle switches and guesses which one defuses the bomb. As Earl takes photos, MacGyver succeeds in shutting off the bomb. However, their relief is short-lived. An unseen trigger activates and MacGyver and Earl dive out of the room. Earl is a second too slow and is caught in the blast and killed.
As MacGyver gets his burns treated, Roswell complains that Rachel will now get what she always wanted: command of the arson squad. Rachel orders Roswell to start working on the psychiatric profile and suggests that Prometheus may be a victim of a fire. They examine the photo and realize the insulated handle is an antenna. Prometheus watched their efforts to deactivate the bomb and used a remote control to activate the fire bomb. Rachel tells MacGyver that he's off the case, blaming him for Earl's death because he insisted on going in. MacGyver refuses to let his friend Earl's death go unsolved and concludes that Prometheus watched them try to defuse the fire bomb from the nearby hotel. When Rachel goes to investigate the bomb site, MacGyver talks to the hotel manager who shows him a room with a view of the fire bomb. Rachel notices MacGyver looking at her and glares angrily at him.
After Earl's funeral, MacGyver talks to his friend's wife Betty. She explains that Earl was obsessed with one particular case, a café fire that took place two years ago. He realized that a woman was the common denominators and that insurance was involved. Betty explains that Earl and Rachel were once friends but Earl got the promotions. Later he disagreed with Rachel about a procedure on a fire and as a result, Rachel's hands were badly burned. As MacGyver leaves, he notices Rachel watching him and she quickly drives away.
MacGyver returns to the quad room and sees the hotel manager leaving. He goes to see Rachel, who has been promoted into Earl's position. She wonders why he's there when she took him off the case, and MacGyver asks if the hotel manager came to see him. Rachel says she did and wants to know what MacGyver learned from Betty. MacGyver agrees to trade and Rachel tells him that the manager remembered that the woman who lived in the hotel room had a boyfriend, but doesn't know who he was. In return, MacGyver gives her the information about the café fire and Earl's suspicions. Rachel admits that her hands were injured and removes her gloves to show MacGyver the burns. However, she dismisses MacGyver's suspicions and says she'll try to find the woman and her boyfriend if she thinks it's worth the time.
MacGyver goes through the files and identifies the woman as Victoria Arnold, who owned a café and died in the fire that swept through it. Roswell confirms that Prometheus used koldexin to enhance the effects of the thermite, and the chemical is used in the processing of newspaper color photography.
MacGyver goes back to the hotel and talks to the manager. The manager admits he told Rachel that the boyfriend worked at a newspaper that's now closed down. MacGyver goes to the newspaper officer and a helpful guard lets him in to examine the files. He finds Ralph Broadman, a color plate engineer who lived at the hotel. MacGyver goes to Broadman's address and finds files showing that the engineer worked in the Army as a demolition expert. There's also an envelope marked "Victoria". Before he can open it, Prometheus slips in and taunts MacGyver. The arsonist goes up the stairs while boasting that he's one step ahead of everyone. MacGyver follows him into a paper storage room and Prometheus slips out behind him. He tells MacGyver that there's another fire bomb in the room and he's set it to go off in three minutes.
Using an ink pen cartridge, MacGyver pushes out the hinge pin on the bomb case and defuses the motion sensor. He cuts the power but a backup magnetic circuit kicks in. With only a few seconds remaining, MacGyver uses a forklift cart to lift up the bomb and push it toward the storeroom door. The blast destroys the door and MacGyver runs out through the flames to safety. He goes back to Broadman's desk and checks the envelope. It has photos of the café fire, including a shot of Rachel and Earl. MacGyver sees something in the photo and takes it outside. Roswell and the fire department arrive and MacGyver heads for the squad room to warn Rachel.
MacGyver runs into Rachel's office and discovers that she's tied to her chair and there's another fire bomb on her lap. The hotel manager comes in and reveals that he's Prometheus. He forces MacGyver to handcuff himself to Rachel's chair and explains that he planted the clues so Rachel would go to the newspaper office and die in his trap. When Broadman explains that he is seeking for the revenge of his girlfriend, MacGyver notes that Broadman was the one responsible for the café fire. Broadman and Victoria burned down the restaurant for the insurance money and Victoria was caught in her own scheme. Earl had almost figured it out from the photos. Broadman denies any responsibility, triggers the fire bomb, and runs outside to watch the explosion. MacGyver uses the pin on Earl's badge to remove the hinge pin and open the case, and then deactivate the motion sensor. When he cuts power, the magnetic switch kicks in, and MacGyver uses the magnet from a walkie-talkie to pull it back open and stop the bomb from exploding. Rachel goes to the window and calls down to Broadman while MacGyver sneaks up and knocks him out from behind.
Later, the police take Broadman away and MacGyver shows her the photo of the café fire. He realized who Prometheus was when he saw Broadman in the background of the photo. Rachel admits that she admired Earl despite their disagreements and would give up her badge and her position to have him back, and MacGyver admits that he knows that about her.