MacGyver arrives at a Phoenix Foundation lab to meet with Dr. Kozby at Koz's request. After he goes in, a masked commando emerges from beneath his jeep and ascends to the roof. As he gets to the top, he clutches at his head in agony for a moment. Below, Pete goes into the classified lab and runs into MacGyver. He's going to see Kozby as well. As they go inside, the intruder descends via an elevator shaft. He drops onto the car as Pete and MacGyver take it down to Koz's lab. Once they're gone, the intruder removes his mask and dons a white lab coat.
Pete and MacGyver run into Kozby, who says that he didn't leave any message with MacGyver. They figure that they somehow crossed their wires. Kozby shows him a bacillus anthracis
sample that he's working on, and which he warns can easily be turned into a biological weapon. Meanwhile, the intruder puts on a pair of glasses and attaches an "out of order" sign to the elevator. He goes into a secure room and dons an anti-contamination suit, then enters the room with the anthrax. As he goes into the room and removes the samples, Koz explains that he's created an advanced sensor that can detect anthrax, but he's gone through his existing funding. The intruder acquires a sample of anthrax and leaves the way he came. The sensors detect the vial's removal and the system shuts down.
The intruder gets the elevator door open and knocks out a scientist who tries to stop him. He puts the vial in a waist pouch then clutches at his head in pain again. Once he's recovered, he climbs up the elevator shaft. Below, MacGyver finds the unconscious scientist and opens the door. He finds the discarded suit and realizes how the intruder escaped. Pete notifies security while MacGyver discovers has pulled his climbing cable up after him. MacGyver jimmies the elevator car battery with his Swiss Army knife and the car ascends. The intruder assembles a launching device and fires a cable over the compound fence and into a nearby pole. He prepares to escape just as MacGyver reaches the roof. MacGyver recognizes the intruder as Steve Morrison, a man who once saved his life. Steve slides down the cable and then cuts it, leaving MacGyver to hang, then leaps onto a passing train.
Pete checks Steve's record and discovers he was honorably discharged from the SEALs five months ago after a month in a non-operational position. MacGyver points out that SEALs consider nonop positions as the next step to forced retirement. The Navy has no record of what happened to Steve after he was discharged. Koz explains the effects of anthrax and how easily it can be spread. Worse, Steve didn't properly house the anthrax and the vial's seal can easily rupture.
Steve is at home and calls his buyers. They agree to a meeting place in an isolated spot. He's unaware that his clients plan to kill him once they have the anthrax.
Pete and MacGyver meet with Steve's former commander, Commander Hilliard. He says that Steve was growing increasingly unstable, leading to his discharge, and reluctantly tells them Steve was part of the SEALs anthrax detection squad. Steve received a head injury from a terrorist bomb while rescuing MacGyver and completing the mission, but Hilliard insists he was checked out as 100% recovered. MacGyver doesn't believe it but Hilliard insists the Navy didn't screw up. They're interrupted when Steve calls Hilliard and tells him to meet him at the house in half an hour. MacGyver goes with Hilliard while Pete calls the police.
Steve's wife Marie pulls up to the house while Steve himself first reviews his medical files in disgust, then grabs his bags (and the anthrax) and goes out to meet his wife. Before he goes out, he activates a light sensor. She assures him the moving truck is on its way and wants to go in the house for a final check. Steve snaps at her and she tries to walk away, and he quickly apologizes and admits she's all he has left. She promises she won't leave him and they leave.
Hilliard and MacGyver arrive at the house a few minutes later. When there's no answer, they carefully go inside. When they break a light beam, a tape player activates warning Hilliard that there's a bomb on the desk, and if they try to leave they'll set off a motion detector that will activate the bomb. However, the bomb is on a two-minute timer and will set off the bomb anyway. MacGyver has Hilliard slide him a floor lamp and then move the light bulb as close as possible to shield his movements. Once the sensor is blinded, MacGyver gets to the bomb and pulls the wires just in time. Pete pulls up outside while MacGyver finds maps of Oregon. As Pete passes on the information to the police, MacGyver finds the Navy's discharge letters and a number of letters that Marie sent to Hilliard that were returned unanswered. MacGyver confronts Hilliard, who says it was between Steve and the VA. MacGyver shoves the letters at him in disgust and leaves.
Steve and Marie are driving to Portland and talking of their future running a fishing charter. Marie warns they can't afford a boat but he insists that he can. They spot a roadblock up ahead and Steve quickly turns around and drives away. He refuses to explain and pulls into a rest area, then tells Marie to stay in the car while he makes a phone call. He tells his buyers, Muller and Felder, to meet him at a nearby summer camp that's closed for the season. In the car, Marie finds the vial of anthrax and confronts her husband. She realizes he stole it but Steve assures her that the police will never catch her. He accuses everyone being against him, including MacGyver and finally Marie. He takes her purse with the car keys and runs to the summer camp.
Marie calls MacGyver and he and the authorities arrive. Marie snaps at Hilliard, accusing him of having no idea about her husband's condition. She tells them where Steve was heading. When Koz hears that the buyers are arriving by helicopter, he warns that any change in air pressure integrity will breach the seal. Marie warns that Steve won't surrender to the police and Hilliard agrees. A biker comes over and asks Pete for $500: MacGyver took the bike and told him to get Pete to pay. MacGyver rides up the trail to the summer camp. Meanwhile, Marie tells Hilliard she wrote to him to get his help in convincing Steve to return to the hospital for treatment. He suffered from lesions caused by the injury, and she says Hilliard could have helped. Hilliard hides behind the rules but Marie isn't impressed.
Steve gets to the rendezvous point as Felder and Muller arrive by helicopter. Meanwhile, MacGyver comes to a heavy tree branch blocking his way. He uses a board as a ramp to jump over it and keep going. The helicopter lands and Steve sneaks up on it. Felder and Muller get out while Steve has more head pains. He calls out to them, demanding the cash. He warns them to stay their distance and then emerges from hiding, holding the anthrax. He has them put down the money and takes it, then puts the anthrax on the ground and backs away. MacGyver arrives on a vantage point above and watches as Felder draws a gun and shoots Steve. He takes the money and heads for the helicopter. MacGyver spots a tire swing and gets back on the motorcycle, then coasts down the hill. He cuts loose the rope from a tire swing, then rides toward the helicopter and throws it into the rear blade. He rides by and grabs the anthrax, but a lucky shot takes out the motorcycle.
Muller and Felder try to circle around while a badly wounded Steve recovers consciousness. MacGyver takes refuge behind a canoe but Steve attacks the two men. MacGyver knocks out Felder while Steve disposes of Muller and takes his gun. He tells MacGyver to hand over the anthrax and insists there's nothing wrong with him. MacGyver tries to get through to him, asking for a chance to save his life in return, and Steve gives up the gun, sobbing.
Later, MacGyver meets Marie and Steve at the hospital as he recovers. Hilliard arrives to wish Steve well and apologizes for abandoning him. Steve says he would have done the same thing but Hilliard says he'll read all of his mail from now on, salutes him, and then shakes his hand. Marie thanks MacGyver for his help and MacGyver tells Steve "welcome home."