MacGyver flies to the Pacific Northwest to the forests where he worked as a chokerman during his college years. He talks with the pilot, who points out how the logging companies are stripping the old-growth trees and doing what they can to cover up their activities. They talk about an upcoming timber summit between the logging companies and the ecological protesters that fell through. MacGyver admits that an old friend of his let him down.
Amy Chandler, a local eco-protester, has organized with others and stopped a truck driven by Braddock. Sheriff Delaney arrives to break up the confrontation and Braddock's boss, Foxworth, arrives to assess the situation. Accompany him is his foreman, Jack. Foxworth, who has a contract for restricted logging on publicly-held lands, insists that he's following the contract. Amy isn't impressed, even when Jack points out that the company keeps hundreds of workers employed and feeds money back into the community. Amy isn't impressed, and Delaney is forced to take her away. As she leaves, Foxworth wonders when Jack is going to do something about his wife. Jack points out that he couldn't, which is why they're separated.
MacGyver arrives in town and sees Amy being taken into the station. As Braddock files out a complaint in the office, MacGyver goes in to see his friend. Inside, Delaney warns Amy that if she doesn't stay away from Foxworth's logging outfit, he'll have to arrest her. Amy insists that the recent death of a worker, Lopez, is tied to Foxworth but Delaney points out that the investigation shows it was an accident.
As Amy leaves, she runs into MacGyver. He's unhappy that she pulled out of the timber summit but she explains that she refuses to deal with criminals and that Foxworth is responsible for Lopez's death. Back at her house, she explains that Lopez was a chokerman who contacted her with a claim that Foxworth was violating his contract. The only thing he would say on the phone was "check Betsy." Before she could meet with him, he turned up dead, the victim of an alleged accident. She refuses to negotiate with Foxworth and MacGyver suggests that compromise is the way to resolve the situation. Amy comments that MacGyver sounds a lot like her husband, and informs MacGyver they separated six months ago. MacGyver finally convinces her to reconvene for the summit in return for his investigating Lopez's death. As they share a friendly hug, they're unaware that Jack has arrived outside, carrying flowers. When he sees them through the window, he turns and leaves, disappointed.
The next day, MacGyver approaches Jack at the logging site and asks for a job. Jack recognizes him from the previous night but doesn't mention the incident. Meanwhile, Foxworth is meeting with Glass, a log broker and a member of the Yakuza. Foxworth is worried that the authorities have ramped up inspections since Lopez's death. Glass, unimpressed, warns that he holds the lien on Foxworth's company and if Foxworth doesn't meet the quota, the Yakuza will put him out of business. When Foxworth tries to defy him, Glass physically threatens him and warns that there'll be worse if Foxworth doesn't meet the delivery schedule.
After Glass leaves, Foxworth tells Braddock to quickly move out the remaining shipments. Braddock warns that the inspectors are getting closer to discover their plan to reuse tags but Foxworth has no choice. They notice Jack hiring MacGyver and Braddock recognizes him from the police station when he came in to see Amy.
As MacGyver works, Jack rides him hard because of his belief he's seeing Amy. During lunch, MacGyver talks with some of the workers, including Braddock. Braddock is hostile toward any kind of a compromise but some of the other loggers are sympathetic when MacGyver suggests a compromise is possible. Braddock gets into his truck and MacGyver realizes that it has mud flaps with the name "Betsyâ€ on them. He chats with one of the workers who explains that the inspectors use the tags to make sure that Foxworth follows the contract, but there's only a handful of inspectors to go around.
Braddock drives into town where Amy is trying to get the townsfolk to mobilize against the logging company. She goes into the bowling alley where Foxworth and Glass are meeting. Braddock meets with them and Foxworth tells them that he's confirmed MacGyver works for the Phoenix Foundation, the organization putting the summit together. Glass tells Foxworth to take care of the situation once and for all. Meanwhile, Amy has approached the head waitress, Meg, and asks her to put up posters protesting the logging company. Meg is reluctant to antagonize her customers, many of whom rely on the company for a livelihood. Braddock and Foxworth come over and taunt Amy. When she snaps back, threatening to sabotage the company's equipment if she has to, everyone in the bowling alley hears her.
That night, MacGyver visits Amy and tells her what he found out about Braddock's truck. She remembers Jack once saying that Glass had a financial hold on Foxworth and finally tells MacGyver that Jack is her husband. Despite feigning an air of unconcern, she's eager to hear if Jack mentioned anything to MacGyver about her.
The next day, MacGyver talks with Jack and explains that he and Amy are old college friends. Jack doesn't believe it and tells MacGyver he saw them together at the cabin. MacGyver tries to reconcile the two, telling Jack that Amy still loves him. Jack admits he feels the same toward her but the logging situation has come between them. MacGyver suggests they try to work out a compromise and it's never too late. Jack starts to ask MacGyver for the truth about why he's there, but an overhead cable snaps, dropping a load of logs. MacGyver shoves Jack out of the way just in time. They inspect the cables and realize that they've been tampered with. Foxworth brings up Amy's comments at the bowling alley and makes sure his men have reason to believe she's responsible, and then calls the sheriff to swear out a complaint.
Delaney searches Amy's cabin and finds a pair of bolt-cutters. He also finds steel spikes like the ones that eco-terrorists put in trees to sabotage logging attempts and endanger the men. At the police station, Amy denies committing any illegal acts and MacGyver and Jack back her. Foxworth, disgusted, fires both of them and leaves. He meets with Glass, who has received orders from his superior to tell Foxworth to dispose of MacGyver, Jack, and Amy. When Foxworth balks at more murders, Glass removes his glove and shows the owner the stump of a little finger. Explaining that he cut off his finger to show his loyalty to the Yakuza, Glass threatens to cut off pieces of Foxworth if he doesn't deliver all of the lumber to his freighter that night.
MacGyver and Jack go to get their clear and spot Braddock stapling old tags on new loads of logs. MacGyver realizes they're up to something but Jack explains that the security surrounding the log shipments, involving tags and brands, is foolproof once the logs are checked in at the scaling stations. When MacGyver confirms the tags are being reused, and Foxworth logs in the tags, they realize that Braddock and Foxworth are both fully involved. MacGyver sends Jack to notify Delaney and find out what properties Glass holds while he rides on the back of Braddock's truck.
Jack goes into town to tell Delaney what's going on, but the sheriff warns that he can't issue a warrant without evidence. As he goes to check the tag receipt records, Jack convinces the deputy to determine what properties that Glass has bought out in the area. Among Glass' holdings is a bankrupt sawmill. Meanwhile, Amy â€˜s lawyer has gotten her released on bail. She runs into Jack, w ho explains what they've learned. Delaney returns with confirmation that Foxworth has been tampering with the tag receipts and Braddock hasn't logged in tags for two weeks. Amy insists they should go immediately but Delaney tells them to wait until he has a warrant. Once he leaves for the judge, Amy convinces Jack to go with her.
Braddock drives his truck to the sawmill and removes the tags, while his assistants cut the branded ends of the logs off and burn them. MacGyver checks out the sawmill office and finds a map showing the location of Glass' freighter. Finally, he spots a trawler outside that ferries the logs out to the freighter. Before he can leave to report his findings, MacGyver spots Amy and Jack sneaking into the sawmill. Before he can do anything, Foxworth captures them.
Foxworth takes the couple into a warehouse and MacGyver sneaks in ahead of them as Glass calls his superiors by cell phone to tell them everything is going as planned. Foxworth arrives with Amy and Jack, and Amy boasts that Delaney knows all about what's going on. Unimpressed, Glass tells them that they're both going to suffer an unfortunate accident. He turns on a wood chipper and prepares to feed them into it. MacGyver swings down and knocks Glass aside, giving Jack the opportunity to disarm Foxworth.
Glass runs outside and MacGyver goes after him. The Yakuza is a skilled martial artist and MacGyver is soon at a disadvantage. He manages to tackle Glass, knocking him into a pile of sawdust. Glass grabs a chainsaw and comes after MacGyver, who manages to hold him off with a fire hose until he runs out of water. Knocking him back, they turn on a conveyer belt crane. Glass draws a knife and attacks MacGyver, falling onto the belt. The two are swept upward, and MacGyver manages to jump clear just in time as Glass goes over the top of the crane and falls to his death many stories below. The police arrive to take Foxworth, Braddock, and their men into custody.
That night, Delaney and his men capture the trawler and the freighter and get everything they need to put Foxworth and Braddock away for a long time. Amy explains that she's the one who insisted that Jack come with her to investigate the sawmill. She finally admits that it's time she needs to compromise, personally and ecologically, and offers to participate in the summit while Jack represents the loggers' side of the issue.