As MacGyver checks a stream for contamination, nearby a hermit, Daniel â€œEarthquakeâ€ Toberman, and his dog Buddy watch as a tanker truck drives by. The drivers, Charlie and Grade, stop the truck near the stream and start pumping contaminated waste from the truck into the stream. Downstream, Buddy drinks from the water and dies as Earthquake looks on in horror. He goes after the men and attacks Charlie, ripping off his mask and getting a good look at his face. Grade grabs a gun and shoots, nicking Earthquake in the leg. Charlie and Grade drive away while, MacGyver, hearing the shot, comes to investigate. He tries to help Earthquake with his wound and manages to convince the hermit to let him help. He offers his condolence on Buddyâ€™s death and Earthquake remembers himself, in military uniform, arriving late for a local funeral. MacGyver insists he needs Earthquake to identify the men, but the ex-soldier refuses to get involved. He thanks MacGyver for his help and limps away.
Charlie and Grade park down the road and remove the fake logo and license plate from the truck. They call their foreman, Dorman, who tells them to come in. They go to their company, ChemCo Waste Disposal, and are greeted by Dorman and his boss, company owner Martin Farber. Farber tells them to dispose of their clothing and then take a legitimate truck with waste to the dumping site. Once theyâ€™re gone, Farber tells Dorman heâ€™s learned who Earthquake is but that he hasnâ€™t made a report to the authorities yet. He tells Dorman to run a complete check on Earthquake so nothing messes up his operation of using legitimate waste disposal as a cover to dump tons of waste illegally.
Later, Earthquake takes a bus into the city. As he makes his way to the Phoenix Foundation, he remembers the crowds in Vietnam during the war. Two muggers come after him, and he easily subdues them using military training. He grabs one of the men and has a flashback to grabbing his superior officer, Dâ€™Angelo, in Vietnam. He tells the mugger to run and then looks at photos of his dead wife and his squad in Vietnam.
MacGyver meets with Pete and the Foundation attorney, Karen Matsuga. The lab has confirmed that the water is contaminated, and the specific trace elements lead to only two companies. One of them uses ChemCo for waste disposal. A background check shows that Farber owns ChemCo through a series of shell accounts. Earthquake arrives and offers to testify against the men he saw. When they note that ChemCo is responsible, Earthquake warns that the disposal truck had a different company logo.
To get the proof they need, MacGyver and Earthquake sneak into ChemCo as deliverymen. MacGyver bluffs his way past the gate guard and Earthquake spots the truck. MacGyver uses a handheld scanner to locate the specific mix of contaminants from the stream. As they go further into the plant, the guard calls Dorman, who realizes that MacGyver and Earthquake are imposters. Meanwhile, Earthquake finds the fake company logo signs, contaminated with radiation. MacGyver wraps them in lead foil from a protective suit and they start to leave. However, Earthquake spots Charlie and attacks him in a rage, struggling with flashbacks of his attack on Dâ€™Angelo. Dorman calls the police and holds the intruders at gunpoint until they can be arrested.
Pete posts bail and MacGyver manages to smuggle the tube of lead foil out. Next they meet with the stage environmental board where Karen has Earthquake testify in court about seeing Charlie dumping toxic waste. Farber cross-examines the hermit and brings up the fact that he attacked Dâ€™Angelo. Karen objects and Earthquake mistakes her for his dead wife. He explains that Dâ€™Angelo didnâ€™t approve of one of his white officers marrying a Vietnamese girl. The commander sent Earthquake on a mission and his wife was killed dead when he returned. Farber accuses Earthquake of killing his wife and Earthquake attacks him. The agency chairman calls for a recess and Farber tells his men to discredit Earthquake once and for all.
Outside, Earthquake blames himself for his wifeâ€™s death but Karen tells him that she was killed in a cross fire and there was nothing he could have done. Earthquake explains that once he got back from Vietnam, he tried to find regular work but almost went berserk when some children set off firecrackers near the diner where he worked. MacGyver insists that Earthquake can control himself and leaves with Karen for the Foundation. Charles and Grade attack and knock out Earthquake. Grade then throws Charlie over a nearby balcony, framing Earthquake for the manâ€™s death. The police spot Earthquake above and MacGyver tries to go to his friend. However, the police have the building sealed off. MacGyver figures that Earthquake will head for ChemCo.
That night, Earthquake sneaks into ChemCo while MacGyver arrives outside. Earthquake spots Grade and knocks him out. MacGyver walks across a high pipe to get into the building. However, security finds Grade and realizes that Earthquake is on the premises. MacGyver overhears them report in and heads inside.
Earthquake goes to Farber's office and tries to take him in. However, Farber is armed and ready and summons Dorman and the security guards to capture Earthquake. They take him to a sealed chamber and handcuff him to some overhead pipes. MacGyver spots them and puts a tire into a truck cabin, then attaches an air hose to slowly fill it. While the tire fills, MacGyver goes to a chemical storage room and fills two jars, one with chlorine and the other with a catalyst.
Farber has Dorman bring in Grade and informs Earthquake that theyâ€™re going to kill Grade, make it appear that Earthquake was responsible, and then shoot Earthquake in â€œself-defense.â€ Outside, the tire bursts, breaking the windshield and distracting them long enough for MacGyver to come in and throw the two chemicals, forming a chemical smoke screen. Farber tries to escape but Earthquake breaks the pipe, goes after Farber, and captures him. He starts to throw him off a catwalk but MacGyver gets there in time to help him regain control of himself. They turn Farber over to the police, who already have an eager Grade ready to confess everything.
Later, Pete, Karen, and MacGyver meet Earthquake at the office. The ex-soldier is ready to go back home to the wilderness and find some peace. However, MacGyver has a gift for him: a new puppy.