MacGyver pulls up to the gate at a Phoenix Foundation laboratory after receiving a call from Dr. "Koz" Kozby to come immediately. As he pulls inside past the security guards, a commando slides out from beneath MacGyver's Jeep and climbs up to the roof. As he reaches the top, he clutches at his head in pain.
Below, Pete is also entering the facility and says he's there to get information from Koz for his reports. He and MacGyver descend by elevator, unaware that the commando is atop the car roof. Once they leave, the intruder drops down into the car, removes his mask, and puts on a white lab coat.
MacGyver and Peter run into the easily-distracted Koz, who doesn't remember calling MacGyver. They go to his lab and he tells them that he's working on Bacillus anthracis, trying to figure out a way to build a sensor that can detect the lethal material. However, he's spent all of his research & development funds on the research, and needs more money for the development.
As they talk, the intruder puts an "out of order" sign on the elevator, then goes into the lab wearing a protective suit. He takes a sample of the anthrax and leaves, but the sensors detect the removal of the material. The underground facility goes into lockdown but the intruder goes back to the elevator, rendering a scientist unconscious when he tries to interfere. The commando ascends up the elevator shaft on a rope then cuts it behind him. MacGyver uses his Swiss Army knife to reroute power to the stalled elevator car, bypassing the lockdown, and ascends up the shaft. The intruder has fired a line over the fence and prepares to slide down it. MacGyver arrives and recognizes the man: Steve Morrison, a SEAL who once saved his life. Steve regretfully tells him not to interfere then slides down the line. When MacGyver starts after him, Morrison cuts the line, leaving him to hang while he escapes on a passing train.
Pete checks Morrison's file and discovers that he was transferred to a non-operational position five months ago and then honorably discharged, and his Navy file ends there. Koz warns them that not only is the anthrax highly communicable, but the vial containing it was intended for laboratory use only. Any substantive change in the environment will break the seal and release the anthrax.
Morrison is at home calling his buyers, Muller and Felder. They agree to meet him at an isolated spot to make the exchange, and plan to eliminate Morrison once they have the anthrax.
MacGyver and Pete go to see Morrison's ex-commander, Hilliard. Hilliard tells them that Morrison was injured in the bombing incident where he saved MacGyver's life, was hospitalized, and then received a clean bill of health. However, after that he began acting erratically, endangering his fellow SEALS. MacGyver wonders why Hilliard didn't keep in touch but the commander insists he followed proper procedure. Hilliard gets a call from Morrison, asking for a meeting at Morrison's house in half an hour. Hilliard and MacGyver go to Morrison's house while Pete calls the police.
Morrison is packing his belongings and the anthrax, then reads his medical files. His wife Marie pulls up outside and Morrison turns on a light beam. He goes out and Marie says all their belongings have been sent on ahead. She offers to go in the house for one final check but he convinces her they're ready to go. When she notices he's acting odd, Morrison snaps at her, then apologizes and begs for another chance. Marie promises that she won't leave him and they go.
MacGyver and Hilliard arrive at the house and go inside. They set off the light beam, which activates a pre-recorded message from Morrison, Morrison tells them that there's a bomb on the desk. It will go off in two minutes, and if they try to leave a motion sensor on the ceiling will set off the bomb immediately. MacGyver has Hilliard carefully slide him a floor lamp, then removes the shade. He has Hilliard hold the light to blind the sensor while he gets to the bomb and defuses it just in time.
Pete arrives as MacGyver finds maps of Oregon where Morrison and his wife were moving to. Pete has the police set up roadblocks while MacGyver discovers letters that Marie sent to Hilliard asking for his help. Hilliard sent the letters back unanswered, and defends his decision by saying it was between Morrison and the VA. MacGyver leaves, disgusted.
Morrison is driving to Portland and talks of how they'll be able to start a charter boat service. Marie wonders why he thinks they can afford it but Morrison insists he can cover it. They come to a roadblock and Morrison reverses and drives away, ignoring Marie's questions. He pulls into a rest area and tells his wife to stay in the car. He calls Muller and tells him that now they'll make the exchange at a nearby summer camp that's closes for the season. Muller says they'll be arriving by helicopter. Marie finds the anthrax among Steve's luggage and asks him what is going on. Morrison boasts that the police will never catch him, and then questions her loyalty. He finally accuses her of betraying him, just like the Navy and even MacGyver. Morrison takes her car keys and runs off to the summer camp.
Marie calls MacGyver from a pay phone. When he and the others arrive, Marie snaps at Hilliard for abandoning her husband. When Koz hears that the buyers will be using a helicopter, he warns that a change in air pressure will breach the vial's seal. Both Marie and Hilliard figure that Morrison won't surrender. MacGyver borrows a nearby motorcycle and follows Morrison up the trail. As he goes, Marie explains that her husband suffered from lesions on the brain due to the explosion, and she needed Hilliard's help to convince Morrison to return to the hospital. Hilliard says that that he followed the rules and there was nothing he could have done, but Marie doesn't believe him.
Morrison prepares to meet with Muller and Felder as they arrive, moving through the underbrush to get close and trying to overcome the pain from his head injury. When they touch down, Morrison tells them to give him the cash. They make the exchange and Morrison backs way with the money. MacGyver arrives just as Felder shoots Morrison, takes the money, and heads for the helicopter. As they prepare to lift off, MacGyver uses the rope from a tire swing to tangle the rotor blades, and then rides by and grabs the anthrax when the buyers emerge.
MacGyver tries to get away but Felder shoots the motorcycle and spends MacGyver tumbling. He takes refuge behind some old canoes. They move in for the kill but Morrison attacks them, giving MacGyver time to take out one of them while Morrison disposes of the other. Morrison grabs Muller's gun and tells MacGyver to hand over the anthrax. MacGyver pleads with him for a chance to return the favor and save his life. Morrison, sobbing, collapses and gives up the gun.
Some time later, Morrison receives the necessary treatment and is ready to leave the hospital. MacGyver is there to drive the now-happy couple home. Hilliard arrives and wishes Morrison will, then apologizes for abandoning him. He salutes Morrison then shakes his head. Marie thanks MacGyver for his help and MacGyver welcomes Morrison home.