At a storage facility, a USAF Snake-Eye missile is delivered to a group of black marketeers. Another group of black marketeers descends from the roof and one of them slips. A gunfight ensues and the intruders escape with the truck and the missile.
At a nightclub, Professor Willis performing on saxophone as MacGyver looks on. After Willis finishes his set, he goes to see MacGyver at the bar. MacGyver wants him to provide him with the glitch he discovered in the Snake-Eye guidance system but Willis refuses. The professor notes that he has one of his students, Kate, looking into the problem and she “accidentally” broke into the Defense Department computers. He insists that Kate is a genius and MacGyver says his people just want to talk to her. Willis insists that she be protected and MacGyver agrees. Willis leaves and two men follow him out. In the parking lot, the men try to abduct him. When MacGyver intervenes, they open fire on him while Willis struggles for the gun. MacGyver sets off a car alarm, scaring off the men, but Willis is accidentally shot and dies in MacGyver’s arms.
MacGyver meets with Pete and explains that Willis’ death was accidental. Pete insists that the new programming is necessary since it makes the missile programmable to attack any target. Black marketeers are hijacking each other shipments and the new programming triples its values. MacGyver goes to find Kate even though Pete warns that Defense Department agents are also after her.
At a remote farm location, the men who tried to abduct Willis report to their boss, Hatcher, who tells them to find MacGyver, who will lead them to Kate.
MacGyver goes to Willis’ classroom at the high school and finds Kate. He tells her he was with Willis when he died and they need to talk about the project. She goes home and he offers her a ride. She shows him the collection of defense satellite info she’s collected. MacGyver warns her she’s in trouble for breaking into the Defense Department computers and Kate gets offensive. They’re interrupted when DoD agents arrive to take her downtown for questioning. MacGyver and Kate’s mother suggest she go and Kate has no choice but to go.
At DoD headquarters, local agent Oslow demands answers and Kate offers to show him how she penetrated the security systems. They let her use the computer, giving her the password to access their systems. As she demonstrates how she penetrated their systems, she secretly accesses their building environmental systems. Meanwhile, MacGyver warns Pete that the DoD isn’t going to get anything from Kate and offers to get everything they want from her if Pete convinces the DoD to release her. Pete agrees and MacGyver goes to get her.
Kate accesses the building systems, shorting out the elevators, locking all the doors, shutting down the power, and sending the computers into overload. Finally she sets off the fire alarms and then cuts all the power. When the emergency generators kick in, Oslow and his man realize that Kate has escaped.
Hatcher talks to his buyer, who demands a demonstration.
Kate returns to Willis’ classroom to find MacGyver going through her computer systems. Kate refuses to cooperate until someone tells her what happened to Willis. She challenges him to find out her password. MacGyver chats with her about her lack of social life and uses the words she focuses on without success. When she complains about the fact she’s ugly, MacGyver tries the password “ugly duckling” and accesses her systems. He tries to console her with the fact that she’s special and she has to be comfortable with it. Kate gives him the rest of the access codes and MacGyver copies the information to disk. As they leave, they find Hatcher’s men waiting for him. MacGyver knocks them back and locks the door, then they run into the next room only to find themselves in a dead end. MacGyver hooks up a sound oscillator to a speaker and stunts Hatcher’s men. However, when MacGyver tries to wheel it out the electric cord pulls out and the thugs knock out MacGyver and take Kate.
After MacGyver recovers consciousness, he figures that Kate thinks like him and left him a clue. He goes back onto her computer and finds a file named “duckling” that lists a specific broadcast frequency. MacGyver has the FAA scan for the signal on Kate’s radio. Meanwhile, Kate is locked up at Hatcher’s base. Hatcher prepares to administer sodium pentathol to get her to tell her what she knows.
MacGyver drives to the coordinates provided and sneaks up on the old farm. Kate has given Hatcher the information and prepares to provide his buyer with his demonstration. Hatcher has his men lock Kate up and drives away with the Snake-Eye missile. Kate hooks up a pair of jumper cables from the power generator to the bars on the window of the room she’s locked in. MacGyver knocks out a guard and finds Kate’s room. The bars are too hot to crawl through so MacGyver uses a discarded aerosol can to spray the bars and cool them down. They drive after Hatcher and Kate blames herself, but MacGyver tells her the trick is to live with it. Kate admits he’s the first real friend she’s had and MacGyver tells her he’s honored.
MacGyver figures that Hatcher is staying in contact with his buyer via radio. He uses the jeep radio and her portable radio, and listen in as Hatcher radios his henchman Larkin with the coordinates on the Clinton Narrows Bridge. A marathon is running that day and there will be thousands of people on the bridge when the missile strikes.
With twelve minutes remaining, MacGyver and Kate find where Larkin has the missile launcher set up and ready to fire. It’s too wide open for them to sneak up. MacGyver sees Larkin’s shotgun and they come up with a plan. They use the jeep’s headlight and binocular lenses to focus the sunlight and a mirror to direct it on Larkin’s shotgun. It explodes, igniting the nearby vehicle’s gas tank. Larkin and his men are knocked out but Hatcher calls on the radio to ask what’s going on. MacGyver tries to bluff but Hatcher sees through his deception and prepares to launch a second missile. MacGyver has Kate fire their missile on an intercept course and she manages to destroy Hatcher’s missile. Hatcher’s buyer is none too thrilled.
Later, MacGyver meets Kate at the nightclub where Willis was performing earlier. She’s improved her clothing and he tells her that the DoD has busted Hatcher and will want her services once she graduates. Kate is more interested in a boy that is attracted to her. She thanks MacGyver for all his help and he promises she’ll see him again.