MacGyver is conducting a study of the Knapp Companyâ€™s impact on the local shore. The company lawyer, Remick, stops by and tries to convince MacGyver that his company wants to preserve the beach to maintain the value of their investment. MacGyver doesn't believe it and warns that his preliminary studies show that the companyâ€™s construction of a new marina will irrevocably erode away the beach. Remick tries to bribe MacGyver by offering him a job as a private consultant. MacGyver, unimpressed, tells him heâ€™s going to the state environmental agency to ask for a three-week delay so that the Phoenix Foundation can do a full environmental impact study. Angry, Remick warns that the delay will cost his company millions in interest and that MacGyver will find out how things really work.
As MacGyver drives away from the beach, a tow truck tries to run him off the road. MacGyver manages to blind the driver with fire extinguisher spray and get away.
At the board meeting, the company owner makes his presentation. MacGyver asks for the three-week delay and the board agrees over Remickâ€™s objections. After the meeting, Pete admits that there was no evidence on the tow truck to indicate who the driver was or tie it to Knapp. Knapp and Remick watch them go and Knapp tells Remick to back off: heâ€™s hired a professional â€œnegotiator.â€
Later, Knapp meets with the negotiator, Deborah, at an art museum. He pays her $1 million, half in advance, to â€œnegotiateâ€ with MacGyver and get him out of the picture. Knapp offers her their file on MacGyver but Deborah insists on doing her own research. When she wonders why Knapp is hiring her, Knapp admits that theyâ€™ve already done a study confirming MacGyverâ€™s suspicions.
Deborah mounts a surveillance operation on MacGyver and breaks into his houseboat. She goes through his personal effects and spots a newsletter with an acid rain article written by Deloris Forchuk. She plants a listening device in a wall socket and goes back to her apartment. She then listens in as MacGyver returns home and plays the guitar, and tries to figure out what the best option is for taking care of him. She decides to try romancing him off the study. She buys outdoorsman clothing and a cheap car and then signs up for MacGyverâ€™s art class. She fakes an accident to get his attention and then shows him her painting of a sea otter. They discuss sea otters and Deborah mentions that she co-wrote the acid rain article with Forchuk. MacGyver invites her out to coffee, and theyâ€™re soon constantly together.
MacGyver continues with the impact study and goes out to the beach to supervise the Foundation scientists. Nikki is rigging explosives for seismic testing and MacGyver harshly tells her to let someone else do it. He apologizes and admits to Deborah that heâ€™s rough on the people he cares about. When she wonders if thereâ€™s anything between him and Nikki, MacGyver says that theyâ€™re just close friends.
Realizing that MacGyver isnâ€™t going to let romance distract him, Deborah goes to Nikkiâ€™s apartment and kills the neighbor dog that sheâ€™s watching. Deborah is with MacGyver when Nikki calls to tell him the news. He tells Deborah and warns her that Knapp is probably involved and that she should be careful. If theyâ€™re striking at people close to him. MacGyver goes to see Nikki, while Pete checks with the police. Thereâ€™s no evidence of who the killer was and they figure that Knapp has hired a professional.
Realizing that MacGyver canâ€™t be scared off, Deborah goes with her final option. She rigs his boat with explosives controlled by a remote detonator. As he leaves for the day, she gives him one final chance and asks him if he wants to go with her on vacation. Deborah insists that the marina will get built some day, but MacGyver refuses to back down. As he drives the boat away, Deborah triggers the explosive and MacGyver is blasted into the water.
Divers laying cable are nearby and manage to rescue MacGyver. Heâ€™s taken to the hospital where Pete, Nikki, and Deborah visit him. The doctor warns them that MacGyver is suffering from temporary blindness brought on by flash burn but heâ€™s otherwise okay. The police are unable to examine the wreckage, which was washed out to sea by the tide. MacGyver is sure that itâ€™s no accident and Pete tells him to rest while he investigates further.
Deborah meets with Knapp, who warns her she only has a few days left to take care of MacGyver before the board receives the impact study. She tells him that she plans to take care of MacGyver in a fake road accident.
Later, Pete brings MacGyver home and fusses over him until Deborah arrives. She tells Pete sheâ€™ll take care of MacGyver and sends him on his way. Once Pete is gone, Deborah says that sheâ€™s made reservations at a lodge in the country and that itâ€™s time for MacGyver to take a break and recuperate.
Nikki and Pete go over the autopsy report on her neighborâ€™s dog and Pete notices that it had lynx hair in its mouth. They realize the killer must be a woman wearing a fur coat and that Knapp has used a female â€œnegotiatorâ€ in the past. Given the facts, the only conclusion is that Deborah works for Knapp. They notify the police and try to call MacGyver on his mobile phone.
In the jeep, Deborah is driving the blinded MacGyver out into the country. The mobile phone rings and MacGyver answers, but a storm prevents Nikki from being heard. Deborah secretly cuts the battery power before Nikki can warn MacGyver and blames the storm. She spots a police roadblock ahead and quickly turns around, claiming sheâ€™s going to find a gas station so MacGyver can call his friends.
Deborah drives the jeep into an empty warehouse and stops. MacGyver realizes something is wrong and Deborah drops the charade. She draws a knife and comes toward him. MacGyver manages to knock her down and crawls behind some barrels. He rips off the bandages covering his eyes but his vision is still fuzzy. Deborah starts searching for him, warning that heâ€™s just delaying the inevitable. MacGyver throws a pipe to make her think heâ€™s run outside. When Deborah goes out into the storm to find him, MacGyver crawls under the jeep, cuts the brake line, and hooks the jumper cables up to the car battery. Realizing sheâ€™s been tricked, Deborah comes back inside, saying itâ€™s nothing personal. MacGyver stands up and she comes toward him. When he hears her step into the puddle of brake fluid, he tosses the jumper cables into the liquid. The electrical shock knocks Deborah unconscious.
Later, Knapp and Remick are at the board meeting and the Phoenix Foundation hasnâ€™t shown up. Remick calls for the board to make its ruling but Pete, Nikki, and MacGyver arrive just in time. MacGyver gives his report and insists that it justifies an 18-month impact study. He accuses Knapp of trying to kill him. When Knapp and Remick deny it, the police bring in Deborah, and she admits that sheâ€™s negotiated a deal of her own to save herself from full prosecution. MacGyver can only look on in anger and disappointment.