MacGyver is checking clean water sources in the wilderness and finding signs of pollution. While he checks it out, a hermit, Daniel "Earthquake" Toberman and his dog Buddy watch as a truck travels up a road. He follows them toward a nearby stream where his dog, Buddy, drinks from the stream where they're dumping toxic waste. Earthquake watches in horror as Buddy quickly dies from the contamination. Earthquake goes after the men and attacks one of them, ripping off the man's mask, while the other one grabs a gun. He shoots Earthquake in the leg, giving his comrade time to get back to the truck. MacGyver has found the dead dog and hears the gunshot. As he goes to investigate, the wounded Earthquake sprays the waste at them and they drive off. MacGyver arrives and convinces Earthquake he's on his side and tends to his wound. Earthquake insists he doesn't need help but MacGyver gets through to him and stops the bleeding.
The drivers stop down the road and change license plates and signs, and one of them, Grade demands that the other, Charlie, call Dorman and tell them what happened.
MacGyver finishes treating the wound and says he's sorry about Buddy's death. As Earthquake talks, he remembers arriving at an Asian funeral and wondering when a woman died. MacGyver insists they go back to the city and report the dumping, but Earthquake doesn't want to get involved even though he can identify one of the men. He starts to hobble off as MacGyver asks him to remember that he works for the Phoenix Foundation if he ever needs help.
Grade and Charlie arrive at the toxic recycling plant, ChemCo Waste Disposal, where their foreman, Dorman, and the company President, Martin Farber, tell them to undergo decontamination. Once they're done, they're supposed to take out a new tanker for legitimate waste disposal. Dorman has already checked and learned that Earthquake was the one who attacked the men and he hasn't said anything to the authorities. Farber boasts that he's turned the operation into a legal cover and doesn't want to blow it now, and tells Dorman to run a thorough background check on Earthquake.
Earthquake takes a bus into the city. As he makes his way through the streets, he remembers his time in Vietnam during the war. Two muggers come after him and Earthquake easily takes care of them. He remembers assaulting an officer in Vietnam and tells the muggers to run. Once they're gone, he takes out photos of himself and his Vietnamese wife, another photo of his squad, and a phone number for the Phoenix Foundation.
MacGyver meets with Pete and staff attorney Karen Matsuga. They've confirmed that MacGyver's samples show high levels of contamination, which can be traced to a company that uses ChemCo for waste disposal. Farber, who runs the operation through several offshore accounts, owns the company. Earthquake bursts in and offers to testify, but warns that the sign on the truck wasn't ChemCo's. He assures them that he can identify Charlie.
Earthquake and MacGyver take a van into ChemCo and pass themselves off as deliverymen bringing in radioactive waste. MacGyver bluffs his way past the gate guard, Owens, and Earthquake spots the tanker truck that he saw in the forest. Earthquake goes to look for Charlie while MacGyver uses an electronic device to scan for the specific mix of contaminants he found in the water. They find a chamber and go inside, unaware that the gate guard has notified Dorman that they're on the grounds. Earthquake finds the fake signs and they wrap them in lead and head back for the truck. As they leave, Earthquake spots Charlie and goes into a berserk rage, throwing him through a door. MacGyver holds off the workers as Earthquake beats on Charlie and has flashbacks to assaulting an officer. Dorman arrives with a gun and stops the fight, and the police arrive to arrest MacGyver and Earthquake.
Pete gets them released and MacGyver gets the evidence out. However, Pete warns Earthquake that they haven't established a case yet. Karen has a meeting with the state environmental agency but Earthquake doesn't think they'll do anything despite the others' reassurances. He goes into court where Karen has him identify Charlie and the sign from the truck. On cross-examination, Farber questions Earthquake and notes that he went berserk and attacked a superior officer, and then was court-martialed. When Karen objects, Earthquake has a flashback to his wife, who looks like Karen. He explains that his commander, D'Angelo, frowned on a white officer marrying a Vietnamese girl. When Farber accuses him of killing his wife, Earthquake attacks him and the agency chairman calls for a recess. Farber orders his men to watch Earthquake and figures they need one more thing to drive him over the edge and discredit him.
Outside, Earthquake admits that he's responsible for his wife's death but Karen explains that she was killed in crossfire while he was away. MacGyver asks for Earthquake's side of the situation and he explains that D'Angelo shipped him out once he learned Earthquake was marrying a Vietnamese girl. He got out after 18 months and went to work at a diner, but when some local children set off firecrackers, he lost control and attacked them. MacGyver insists that Earthquake cares and that he can control himself, and that he's no killer. Earthquake stays behind to sort some stuff out in his head while MacGyver drives Karen back to the Foundation. Once they're gone, Charles and Grade attack him. They knock him out and then Grade throws Charlie over a nearby balcony to frame Earthquake. MacGyver and Karen are down below and look up to see Earthquake get up. As the police arrive, MacGyver tells Earthquake to stay put but the police seal off the building and refuse to let MacGyver in. He figures that Earthquake is heading for ChemCo.
That night, Earthquake sneaks into the waste disposal plant while MacGyver pulls up outside. Grade arrives and Earthquake captures him and knocks him out. MacGyver climbs up one of the tanks and walks across a pipe to get into the plant. Inside, Earthquake avoids the guards but Owens finds Grade's unconscious body. Owens calls Farber, who figures it's Earthquake. MacGyver is overhead and hears the conversation. He gets inside while Earthquake finds Farber. However, Farber is armed and his men are ready.
MacGyver arrives as Farber and the others usher Earthquake out of the building. He follows them as they take Earthquake into a pumping station and handcuff him to some pipes. Outside, MacGyver puts a spare tire in the cab of a truck and then uses an air hose to slowly inflate it. He then slips inside and finds chlorine supplies that he mixes with a catalyst. Meanwhile, Dorman brings Grade into the room and Farber explains they're going to kill Earthquake after making it appear he killed Grade.
MacGyver dons a gas mask while Earthquake puts up a fight. The tire bursts the windshield, distracting Dorman and letting MacGyver toss in the two jars of chemicals, creating a toxic cloud of smoke. Earthquake breaks free and goes after Farber while MacGyver subdues the others. He arrives just as Earthquake prepares to toss Farber over the railing. With MacGyver's help he manages to get control of himself. Grade is eager to turn state's evidence against Farber and Dorman.
Later at the Foundation, Pete assures them they've put all of Farber's companies out of business. He and Karen thank Earthquake, who says he plans to go home. MacGyver arrives to provide him with a ride... and a new dog.