MacGyver is at the beach checking coastal flight patterns of birds when Mr. Remick, the lawyer for a local company, arrives. He insists his company wants to preserve the beauty of the land while building a breakwater for a new marina. MacGyver isn't convinced, noting the Phoenix Foundation has found evidence to the contrary. Remick offers to pay MacGyver to come on with his company as a private consultant. MacGyver laughs at him and tells him he'll be going to the board for a three-week extension to get enough evidence do a full impact report. Remick warns him he'll find out how things really work and departs. As he goes down the road, he signals to a tow truck. As MacGyver drives by, the tow truck pulls out after him, closes in, and tries to run him off the road. MacGyver uses a fire extinguisher to blind the driver and escape.
Later, Remick's company Knapp goes to the state environmental agency and Knapp makes his presentation. MacGyver asks for more time and Remick objects. Knapp informs him that he'd end the project if there was any risk of environmental damage and agrees to the delay. After the meeting, Pete notes that they should have brought up the truck incident but Nikki Carpenter warns that they have no evidence and the truck was reported stolen. As Knapp and Remick watch them go, Knapp tells Remick to back off and he'll take a different approach. Later, Knapp goes to an art museum to meet with Deborah and arranges to pay her $500,000 to convince her to "negotiate" and take MacGyver out of the way. She insists on doing her own research and wonders if he really needs her services and Knapp explains that he's already done a survey that confirms all of MacGyver's suspicions are correct.
MacGyver continues his survey as Deborah watches him from a distance. She then breaks into his houseboat and discovers a newsletter on acid rain by a Deloris Forchuck. She takes pictures of it as the phone rings and Nikki leaves a message. Deborah plants a listening device in a wall socket and leaves for her apartment. Once there, Deborah goes over her surveillance photos and starts creating a dossier. She hears MacGyver return home and listens as he plays the guitar. Deborah ponders her options, including, scaring, buying, or romancing him off.
The next day, Deborah continues to listen in as MacGyver prepares breakfast and gets a call from Pete saying the Foundation didn't find any fingerprints on the truck. She dons common clothing and buys a cheap Volkswagen, and then goes to MacGyver’s art class. She gets next to him and starts painting a sea otter, then stages a minor accident to draw his attention. They start discussing sea otters and the fact they're on the endangered list, and brings up Deloris Forchuck's articles, claiming she's a friend who helped write the acid rain article. MacGyver offers to get together and have coffee and they soon end up romantically involved. They discuss his work on the survey and how his life was endangered in the tow truck incident. She wonders if it's worth it and he insists that it is. At the beach, he notices Nikki plant explosives and insists that it's a job for the experts. Nikki introduces herself to Deborah, who notes that MacGyver was a little rough on her. He insists he's rough on people he cares about when they're in danger but they're only good friends.
Deborah decides to strike at Nikki to scare MacGyver off. She goes to Nikki's apartment and kills her neighbor's dog that she's watching. Later, MacGyver is with Deborah when Nikki calls and asks him to come over because of the dead dog. MacGyver explains to Deborah and figures that Knapp's company is involved. He worries that Deborah might be next and she tells him to take care of Nikki. The police don't find any evidence but Pete and the others figure that Knapp has hired a professional. Meanwhile, Deborah a remote device and considers the option of killing MacGyver off.
Later, Deborah suggests they go away somewhere and MacGyver drop the matter. She claims Knapp will get the marina built no matter what. MacGyver insists they're all in it together and he won't let them stop him. He assures her they'll go away some day when it's all over. He takes a boat out while Deborah watches. Once he's far enough out on the water, she activates the remote and sets off an explosion, destroying the boat and throwing MacGyver into the water.
MacGyver is taken to the hospital and Pete and Nikki find Deborah waiting for news. The doctor tells them that MacGyver is okay but is suffering from temporary blindness due to flashburn. They go in to see him and Deborah is properly concerned. MacGyver is sure the explosion was no accident but Pete admits that most of the wreckage was washed out by the tide. He tells MacGyver to rest while they investigate the matter further. Deborah then meets with Knapp, who warns they only have a few days left. She insists she'll handle the matter and plans to dispose of MacGyver in a fake road accident.
Pete brings MacGyver home and MacGyver insists he'll be okay on his own. Deborah arrives and MacGyver insists that she'll be taking care of him so Pete doesn't need to worry. Once he leaves, Deborah says that she's made reservations for them at a country lodge that night and MacGyver agrees to go.
Nikki gives Pete the autopsy report on the dog and he notices lynx hair in its mouth. They figure the killer was a woman wearing a lynx coat and that Knapp has used a woman in the past. They conclude Deborah must be the killer and call the police and the houseboat, but MacGyver has already left. They try MacGyver's mobile phone and MacGyver answers it. Nikki starts to talk but Deborah secretly cuts off the battery as they drive through a lightning storm, and then blames it on the weather. Deborah spots a police roadblock up ahead and then suggests they go back to a gas station so he can call Pete and Nikki. She pulls into an abandoned warehouse and they get out, and he soon realizes something is wrong. She draws a knife and comes after him, but he hits her and blindly crawls to cover.
As MacGyver rips the bandages off, Deborah comes after him and warns that he's only prolonging the inevitable. He grabs a pipe and throws it away to draw her attention toward an outside door. As she goes outside, the partially blinded MacGyver crawls to the jeep and manages to find the jumper cables. He attaches them to the underside of the jeep and the battery and then opens the valve on the brake fluid. Realizing she's been tricked, Deborah comes back into the warehouse and tells him that it's nothing personal. MacGyver blocks the leak with a piece of glass and then places the jumper cables in the fluid.
Deborah finds the discarded bandages and MacGyver stands up and calls out to him. She comes toward him, saying she gave him every chance to back out but he refused to give in. She steps into the brake fluid and MacGyver tosses the jumper cable into the liquid, shocking her unconscious.
Later, the state environmental agency meets and everyone waits for the Phoenix Foundation to arrive. Remick asks for the agency to make their ruling. However, Pete, Nikki, and MacGyver arrive. Pete apologizes and MacGyver says that his survey justifies the 18-month impact study. They have Deborah brought in under police custody and reveal that she's agreed to testify in return for a better deal.