In Paris, France, a team of buyers is reviewing the file on David Crane. Their man will accompany Crane and bring him to them. They wonder if Crane will be able to meet their needs and confirm that he conducted a major theft of U.S. intelligence information for their organization. They're concerned that his attitude is strange but figure that it is typical for a man of his skills to have certain eccentricities. Crane arrives and jokes about his credits, then notes the pieces of the missile are scattered across the country. He plans to use the bureaucracy against the government to steal the missile. Crane then shows the buyers a series of seemingly harmless components he's gathered and assembled into a detonated to trigger a hidden explosive in a chair. When they wonder if they can trust him, he points out that he could have rigged any of their chairs. Crane then tells them to send a seaplane to a lake at a designated time.
MacGyver checks a model town at a Phoenix Foundation test site. He'll guide the Moloch missile through the streets to hit a precise target, using a system that translates verbal commands into code. The general in charge, Abel Makepeace, is less than impressed with MacGyver's casual attitude. The missile launches and MacGyver guides it through the mock town to a successful hit. Makepeace and Pete congratulate him, and Pete notes that the same speech conversion circuitry is useful in another project. MacGyver and Pete go to the Hansen School for the Deaf. The head teacher, Carrie Linden, has a brief vision of MacGyver pushing her out of the way of a truck driven by a man she doesn't recognize (Crane). Pete and MacGyver then have one of the deaf children, Marion, try the device. It works, giving her hearing for the first time. It works,
That night, Carrie has the same dream, except this time she sees MacGyver being hit by the truck. She then sees lightning on a clear day striking nearby and a man on a horse chasing them. Finally she sees a man with a gun opening fire at the horse. In the dream, she and MacGyver run to a grave where she sees a metal skeleton. They dive into the ditch as the horseman jumps over them. On a nearby lake, an older-style car driven by Crane goes across the lake and onto the beach. MacGyver shoves her out of the way and Crane smashes MacGyver down. Carrie wakes up, screaming.
In Battle County, South Carolina, Crane and one of his men are disguised as state patrolmen. They pull a military truck over and two of their men secretly replace a box of missile telemetry with one of their own. Once the men are clear, Crane sends the truck on its way and warns his men that they have several more operations to conduct across the U.S.
Carrie visits MacGyver at his apartment and tells him about his dream. He figures everything she dreamed relates to things she saw in real life. MacGyver suggests she talk to some sleep-experiment experts but Carrie declines.
At a Veteran's Military Museum in Indiana, Crane and his men knock over a case and then remove another component from a display of the Moloch while the patrons are distracted. They're off to get the guidance system at the Phoenix Foundation facility in California.
Pete and MacGyver finishing eating at an Indian restaurant and MacGyver tries to convince Pete to use the Foundation money to do dream research with Carrie. Pete finally gives in but they're interrupted when a van goes out of control and almost hits them. As the man drives away, MacGyver notices that there are lightning bolts on the van, just like the lightning bolts in Carrie's dream. Pete figures it's a coincidence but MacGyver insists there's something to Carrie's dreams.
At the Phoenix Foundation, Dr. Janice Green hooks Carrie up and then gives her a sedative. They check her brain wave patterns while she describes her dream so they can determine if its' coming from her memories. Carries describes the dream again, describing the lightning, the Moorish warrior on horseback, the metal skeleton in a grave, a man shooting at them, an old car out of the lake, and MacGyver being run down and killed. Dr. Green notes that the patterns don't correspond to anything they've seen before. Carrie insists it's a painful memory, not a dream, and Pete cancels the dreams for the day. Carrie notes that she met MacGyver for the first time at the test site a month ago and they decide to go back there to see if she remembers anything further.
Crane and his men drive up to the Phoenix test site and get in using forged IDs. Pete, MacGyver, and Carrie are already there seeing if she recognizes anything. Crane distracts the technicians while his men steal the fourth and final component and replace it with a fake to cover the theft. However, Carrie spots Crane and recognizes him. When she points him out, one of Crane's men, Brown, opens fire and Crane takes out the tires of the other cars as well as the radio. They escape, leaving the man who opened fire. MacGyver goes after him and manages to tackle Brown, but Crane shoots and kills his own man to cover their escape .
Back at the Foundation, MacGyver realizes that the guidance system is a fake and concludes that the thieves have already stolen the other parts of the Moloch missile. Makepeace starts tracing any facilities while MacGyver wants to keep working on Carrie with her dream. Back at his apartment, MacGyver uses his computer to create an overhead view of the lake from Carrie's dream. MacGyver then runs the shape through the computer and matches it to Braden Lake. They drive there and it's exactly like the lake in Carrie's dream. She also remembers that she's been there hiking, but doesn't remember anything else there from the dream. They retrace the steps of her dream into the nearby woods and spot a rearview mirror lying in a field. They also find the remains of a car lying in a ditch and Carrie realizes it's metal skeleton from her dream. A Moorish man rides up on a white horse: a local stable owner. He hasn't seen any old cars but does remember seeing some men nearby. Crane's man Gorman spots them and opens fire. He contacts Crane by radio, and Crane tells him to chase Carrie and MacGyver toward him. MacGyver and Carrie run to the lake where Crane comes at them in a hovercraft. Carrie trips and MacGyver goes to help her, and Crane rams him with the hovercraft. Gorman arrives, grabs Carrie, and gets her into the hovercraft, and they make their escape.
MacGyver is only stunned from the impact and wakes up a minute later. The Moorish rider arrives and tells him what happened, and MacGyver asks him to call the Phoenix Foundation while he goes after Carrie. Meanwhile, Pete and Makepeace have confirmed the theft of the other missile parts. The only thing missing is the missile body, but Pete discovers that Crane has forged papers to buy a missile.
Crane and his men have returned to a nearby cabin and are assembling the missile parts. Before they rendezvous with the buyers, Crane wants to know how Carrie recognized him and who else knows. Carries tries to bluff her way out by pretending not to speak, but Crane doesn't fall for it. Meanwhile, Pete and Makepeace identify Crane as former CIA and the dead man, Brown, as a military security guard. They get the call about MacGyver and head out.
As Crane tries to get information from Carrie, he snaps at his men, nervous that the buyers will skip the rendezvous if they haven't assured the area is secure. Meanwhile, MacGyver knocks out one of Crane's men, Thorn, as he prepares the hovercraft for departure. MacGyver ties up Thorn and then knocks him out as Gorman comes outside. Gorman assumes Thorn is getting the reserve fuel and goes back inside. While Crane and Gorman prepare to dispose of Carrie and leave, MacGyver gets to the window and uses sign language to give Carrie a message. Carrie then stalls for time by telling Crane about her dream and subconsciously remembering Crane at the test site a month ago. Meanwhile, MacGyver creates a crude water clock by filling plastic bags with water, puts them on a balance beam, and then strings them to the ignition switch on the hovercraft. He then punctures one bag, so that the balance beam lowers and pulls the string.
Crane wants to know what Carrie has told the Foundation and the military and has her repeat her story. Meanwhile, MacGyver goes back to the cabin and strings a rope across the cabin door and makes a lasso. The hovercraft activates and MacGyver snares Gorman when he comes out to investigate. MacGyver then leaps through the window and tackles Crane, and then stuns him with a coffeepot. Pete and the authorities arrive by helicopter to take the crooks into custody.
Later, MacGyver and Carrie are dancing at MacGyver's apartment. MacGyver bends in for a kiss... and Carrie comes out of her daydream. She's at the school with MacGyver, and Pete arrives to tell them that they captured the buyers and Crane and his men are confessing to everything. The Foundation will continue to finance the speech-research project for the deaf school. Two students come over and take MacGyver over to Marion, who speaks and thanks him.