In Paris, France, a council of international espionage brokers is meeting with David Crane, an ex-CIA agent who specializes in procuring top secret information. The council wants Crane to conduct a theft of a piece of U.S. intelligence information but are concerned about Crane's reputation for eccentricity. When Crane arrives, he explains that the pieces of the missile they want are scattered throughout the U.S. but he plans to use the U.S. government bureaucracy against it. As an example, Crane assembles several seemingly harmless pieces that he bought at electric stores in Paris, and creates a detonator. He demonstrates it by blowing up a chair in the room. When the council questions his loyalty, he points out that he could have planted a bomb in any of their chairs. As they look nervous, Crane tells them to have a seaplane ready at the designated lake at the proper time to pickup the missile.
The Phoenix Foundation is working with General Abel Makepeace to test their new guidance system on the military's Moloch missile. The Foundation's contribution to the system is a voice-input system that translates spoken words into electronic guidance code. MacGyver and Pete are at the mock town the military has set up, and MacGyver is verbally guiding in the missile for a precision strike. The missile strike works perfectly, but the verbal input system has another use. Next, Pete and MacGyver go to the Hansen School for the Dead, where they're helping deaf children hear. The head teacher, a deaf woman named Carrie Linden, sees MacGyver and realizes he's part of a dream she's been having where he saves her from being run over by an antique car. MacGyver and Pete have one child, Marion, test the system and give her the gift of hearing for the first time in her life.
At home that night, Carrie has the same dream again. In her dream she sees herself and MacGyver running through the woods on a clear day. A bolt of lightning strikes a nearby tree, and then a Moorish warrior on a white horse rides chases after them. They come to a grave containing the metal skeleton of a giant. They leap into the grave, avoiding the horseman, but an unknown man drives an antique car across the surface of a nearby lake and then hits MacGyver, seemingly killing him. Carrie wakes up from the dream, screaming.
In Battle County, South Carolina, Crane and his men intercept a military truck. Crane and one of his men are disguised as state patrolmen. While they delay the driver, Crane's other two men secretly replace a crate in the back with one of their own. Crane then sends the truck on its way and he and his men head off to the next component.
Carrie visits MacGyver and tells him about her dream. He doesn't believe in psychic abilities but concludes that somehow her subconscious is tying together things that she saw in real life and trying to warn her. He suggests that she talk to sleep-research scientists at the Foundation but Carrie is reluctant to do so.
Crane and his men conduct a similar operation at a Veteran's Military museum in Indiana. While Crane goes in disguised as a janitor and knocks over a case, his men switch out a guidance part from a display missile and insert a fake replacement. They then depart for the test facility in California.
MacGyver and Pete emerge from an Indian restaurant and discuss Carrie's situation. Pete is reluctant to finance tests but finally gives in. An out-of-control van almost hits them, and MacGyver points out that it has lightning decals on the side. Pete believes it's a coincidence but MacGyver isn't so sure. At the Foundation, Dr. Janice Green gives Carrie a sedative and hooks her up to a monitoring device, comparing what she's describing to her memories. Carrie describes the dream again and Dr. Green admits it doesn't correspond to any readings they've seen in the past. Carrie is sure that what she's seeing feel like painful memories, not dreams. They figure that since MacGyver is so significant in her dreams, it somehow relates to him. Since Carrie met MacGyver a month ago at the test site, they go back to the test site.
At the mock town, Crane and his men arrive and use forged Ids to get in. Pete, MacGyver, and Carrie are already there, going over the scene to see if she recognizes anything. Crane uses his same basic plan of distracting the security while his men make the switch. However, Carrie spots Crane and recognizes him as the man who runs over MacGyver in her dream. She points Crane out and he has his men shoot out the radio and the tires on the vehicles present. MacGyver manages to tackle one of the men, Brown, but the others drive away in their van, and Crane kills Brown so he can't expose them.
Back at the Foundation, MacGyver discovers that the Moloch missile guidance system part is a fake. They figure that Crane and his people have made similar switches, and that it's possible to bypass security by stealing the individual parts in widely different locations. While Makepeace tries to locate the stolen parts, MacGyver thinks Carrie's dream is the key to finding Crane. He has her describe the lake from her dream and he recreates it on his computer, and then feeds it into a nationwide database. They identify it as Braden Lake in California. When they arrive their Carrie recognizes the landscape as exactly the same as in her dream. She realizes that she has been hiking there in the past. They retrace her steps from the dream and find a ditch filled with a wrecked car: the "skeleton" from Carrie's dream. A Moorish man on a white horse rides up: he's the owner of a local stable. He remembers seeing Crane and his men in the vicinity.
As they talk with the stable owner, MacGyver and Carrie are unaware that Crane's lieutenant Gorman is watching them. He calls Crane by radio and then opens fire on MacGyver and the woman. They run to the lake where Crane intercepts them: driving across the lake in a hovercraft. He rams MacGyver, seemingly killing him, and then captures Carrie and leaves.
MacGyver is only stunned from the collision. He has the stable owner call the Foundation while he goes after Carrie. At the Foundation, Pete and Makepeace have learned that the other missile parts are missing and that Crane forged papers to purchase the missile body. The thieves now have the completed missile.
Crane and his remaining men are holed up at a cabin near the lake. They're ready to meet with the buyers and hand off the missile, but Crane wants to find out how Carrie recognized him. She tries to pretend she can't speak but Crane remembers that she pointed him out at the mock town and doesn't fall for it.
At the Foundation, Pete and Makepeace have identified Crane and the dead henchman, and receive the call from the lake.
MacGyver follows the lakeshore to the cabin and knocks out Thorn, one of Crane's men. MacGyver then sneaks up to the cabin and hand-signs a message to Carrie to stall for time. As she does so by slowly explaining about her dream, MacGyver rigs up a water clock with plastic bags and branches, then ties them to the hovercraft's ignition switch so it'll go off while he's at the cabin.
While Crane goes over Carrie's story, MacGyver sets a snare in front of the cabin door. When the hovercraft turns on, Gorman comes out to investigate and is snared. MacGyver jumps through the window and tackles Crane, knocking him out with a handy coffeepot. The authorities arrive by helicopter to arrest Crane and his men.
Later, Carrie is at the deaf school having a daydream that she and MacGyver are sharing a candlelit dance at his apartment. Before they can kiss, she snaps out of her daydream. Pete and MacGyver are there and Pete confirms that Crane and his men confessed to everything, and the council members were arrested when they arrived to pick up the missile. The hearing-restoration program is a success and Marion speaks her first words, thanking MacGyver for his help.