The owner of the Smoke Creek Farm, Kyle Larson, is meeting with local gangster George Henderson that he won't be fixing any more races for him. When Kyle throws a jockey's crop on the ground, Henderson's assistant Mick Underwood quickly picks it up and tells him to be careful with it. An angry Henderson throws Kyle in a stable with a horse and then activates the electronic device hidden in the crop's handle. The horses go berserk and Henderson lets Kyle get stomped to death by the horse in the stable with him. When they hear Kyle's daughter Jenny coming, Henderson and Underwood escape while she discovers her dead father.
MacGyver and Jack Dalton return from a mission to Mexico to find pottery. MacGyver isn't happy Jack's dragged him off on another moneymaking scheme, and Jack isn't thrilled that MacGyver dumped their cargo so they could make an escape. They discover that Jenny has left them a phone message about her father's death, and the fact she doesn't believe it was an accident.
The guys go to the farm to help and Jenny explains how all of the horses went berserk that night. She has also found a small micro-transmitter on the floor except one. Jenny explains that her father Kyle was in debt to Henderson, who forced him to fix races after buying out the farm's mortgage from the bank. Kyle told Jenny he was finally going to stop working for Henderson the night of his death. At her father's funeral, Henderson tried to buy Jenny's Chance from Jenny.
MacGyver notices that every stable was damaged by the berserk horses except for Jenny's Chance. Jenny notes that the horse is deaf and MacGyver tests the micro-transmitter by hooking it into the stable's intercom system. It gives off a high-pitched tone that drives all the horses but Jenny's Chance berserk. They figure that Henderson is responsible but need proof.
Henderson checks on Underwood, who is making a new micro-transmitter to replace the missing device. He tells Underwood to have it ready by the race the next day.
MacGyver and Jack check with Pete, who has run a background check on Henderson. Henderson is laundering money for Lucky Charlie, a Cuban drug lord. Pete calls in FBI agent Colin Yardrow, who explains that tried to run a sting operation on Lucky Charlie using $1.5 in FBI money, but he escaped with the bait. He explains that lucky Charlie and Henderson have never met face-to-face and has tapes of their conversations. MacGyver and Jack figure out a way to scam Henderson out of the money and get him to confess to Kyle's murder.
Pete and Colin go to Henderson. Pete claims to be Harry Boyle, a horse buyer. He offers Henderson $200,000 for Jenny's Chance and Henderson refuses to sell. Pete gives him a day to reconsider and says he'll be at a bar, the Derby Grill. MacGyver, Jack, and Jenny are watching via binoculars and watch Underwood as Henderson sends him to tail Pete. They follow Underwood to the bar, which is a FBI cover operation. Underwood goes in and watches a staged conversation between Pete, Jenny, and MacGyver, with MacGyver pretending to be a computer nerd named Dexter Filmore. Pete tells "Dexter" to get the micro-transmitter working, loudly enough for Underwood to hear. Jenny reminds Pete that they need her horse to make his plan work.
Once the trio goes downstairs to watch a horse race, Underwood calls to tell him the place is a bookie joint. Henderson comes to the bar to check it out. Afterward, Jack visits Henderson at the farm and, sporting a Cuban accent, claims to be Lucky Charlie. He explains that he's on the run from the FBI and needs his entire $1.5 laundered by the next day so he can make his escape. When Henderson warns he can't do it in time, Jack says he has someone else who can and Henderson reluctantly gives in.
Realizing "Dexter" is involved, Henderson and Underwood snag him at the bar and take him back to the stables. Underwood finds his micro-transmitter plans and shows MacGyver his own unit. Henderson throws him in a stable and uses his micro-transmitter to drive the horse berserk. MacGyver gives in and tells them that he's a computer expert but he couldn't make the device to Pete's specifications. What he has done is set up Pete's computers to run his bookie operation. Henderson and Underwood take MacGyver to the bar and they go downstairs to the gambling parlor in the basement. The FBI team is running tapes of races and Jack is there as well, negotiating with Pete to launder his $1.5 million. Pete claims he can launder Jack's money on time and has MacGyver explain that he uses his computer system to bet the money a nanosecond before the betting closes to avoid changing the odds. They then collect from the losers, pay off the winners, and launder the money. Pete offers Jack a 6-to-1 payoff on his $1.5 million, but Henderson warns that they need Jenny's Chance and his micro-transmitter to guarantee a win. Pete reluctantly agrees to bring Henderson in and offer him a 50/50 split.
That night, the team reviews the plan but Colin comes in with bad news: Lucky Charlie was injured after he was spotted by the police, but managed to escape. The FBI was unable to put a seal on the news before it got out and Henderson now knows he was injured.
The next day, Jack goes to the arm sporting a (fake) bullet wound. Henderson has his money, but the real Lucky Charlie comes out with the same injury. The crooks demand to know if Jack is working with Pete, and Jack explains that he's trying to scam Pete. They prepare to kill him but Jack warns that Pete will be expecting him, not the real Lucky Charlie. Henderson reluctantly takes him along with them as they go to the bar.
At the bar, MacGyver is dressed up as Dexter and situated in the monitor room. Henderson and Lucky arrive with Jack and the drug lord's $1.5 million. They tell Pete that Jack is a conman and have him locked up. He figures they're working with Jack but Lucky Charlie insists that Pete go through with the deal. He gives Pete the money and MacGyver and Colin count it… as well as confirm it's the marked money from the FBI sting.
The race begins on the big screen but Lucky Charlie says he was in Florida and saw it from his box at the track a week ago. He shoves Pete into a table, revealing a hidden VCR. Lucky Charlie shuts off the machine and the race disappears from the screen. Lucky Charlie thinks the entire thing is a set up and Henderson is in on it. As the mobster denies it, Lucky Charlie angrily picks up a chair and throws it at a mirror. It shatters, revealing Jenny, who has been watching the entire thing through the two-way glass. Jack lunges at Henderson, who shoots and kills him. Jenny accuses Henderson of killing Kyle, and the mobster admits he killed her father.
At that, Pete says they've got what they want. The man dressed as MacGyver dressed as Dexter reveals that he's Steve, an FBI agent who has been recording the entire exchange. FBI agents arrest Henderson, while Jack gets up, alive and unharmed. Lucky Charlie removes a mask: he's MacGyver, who switched Henderson's gun for one with blanks at the farm. Pete explains that they arrested Lucky Charlie an hour after the news story, and sent in a disguised MacGyver. They play back the recording of Henderson confessing to Kyle's murder and celebrate while he's taken away.