Black market arms dealers steal two U.S. Air Force Snake-Eye missiles, only to have a rival group steal the missiles from them.
MacGyver goes to see his old mentor Professor Willis, who is performing saxophone at a nightclub. DXS has sent MacGyver to get Willis' help: his student, Kate Lafferty, helped him research problems with the Snake-Eye missile's guidance system. She broke into the Defense Department's computer systems to help her teacher. Willis is reluctant to turn her over to the government, but MacGyver says that the DoD just wants to talk to her. Willis leaves, but two criminals go after him in the parking lot and try to abduct him. MacGyver comes running, and they open fire. Willis struggles with one of the men, Larkin, who inadvertently shoots him. The crooks flee, and Willis dies in MacGyver's arms.
MacGyver gives Pete Thornton a report on what happened. Pete warns that with the new programming developed by Kate, the surface-to-air missiles can be programmed to go after any target, in the air or on the ground. Crooked arms dealers are eager to get the new programming, which will triple the value of their stolen goods. Pete warns MacGyver that the DoD is also looking for Kate.
Larkin and his accomplice report to their boss, Hatcher, who is using an abandoned barn as a base of operations. Hatcher knows that MacGyver has been assigned to find Kate and tells them to follow MacGyver to the girl.
MacGyver finds Kate at Willis' high school oom. Angry at her mentor's death, Kate refuses to discuss the guidance system and goes home. MacGyver offers her a ride, meets her mother, and notices that Kate has tracked dozens of satellite systems. Kate takes offense when MacGyver warns her she's in trouble for breaking into the DoD computers. DoD agents arrive to take her in for questioning. MacGyver verifies their credentials and advises Kate to go with them to the Federal building. The local DoD agent, Oslow, interrogates Kate, and she offers to show him how she hacked into the system. They provide her with their password, and as she enters the system, she secretly taps into the environmental systems.
At DXS, MacGyver warns Pete that Kate won't tell the DoD anything. He cuts a deal with Pete: he gets Kate to tell them the flaw in the guidance system and the new programming, and Pete convinces the DoD to release the girl. Pete releases the girl, unaware that she's already sabotaged all of the Federal building's systems and made her escape.
Hatcher's buyer meets with the arm dealer and demands a demonstration of the reprogrammed missiles before he makes the purchase.
Kate goes back to the high school and finds MacGyver trying to find the password to access her files. She challenges him to do his worst, and he chats about her lack of a social life. As she says certain words, he enters them as passwords without success. Kate complains about how all the boys are intimidated by a girl with brains, and how she's ugly. When she abruptly cuts herself off, MacGyver tries the password "ugly duckling" and gains access to the files. He tells her that she's not ugly and in fact is special. Kate directs him to the file, and MacGyver copies the information.
Hatcher's men arrive, and MacGyver manages to knock them back. He and Kate take refuge in a lab where he hooks up an oscillator to a stereo speaker. When the two men enter, MacGyver and Kate don ear mufflers and deafen them with amplified sound. However, when MacGyver tries to maneuver the speaker out the door, he unplugs the speakers. Hatcher's men recover, knock out MacGyver, and leave with Kate.
When MacGyver regains consciousness, he figures that Kate thinks like him and would have left a clue. He checks her computer and finds a file named "duckling" that tells him to use a communications satellite to scan for a particular frequency. MacGyver gets the FAA to scan western California, and they pinpoint the signal.
Kate is sending the signal on her portable radio when Hatcher and his men come in. He warns her that if she doesn't tell him what he wants to know, they'll use sodium pentathol.
MacGyver drives his Jeep to the coordinates and finds the barn. Hatcher has his men lock up Kate, then sends Larkin with one missile to perform the demonstration, while he takes the second missile to a separate location. Kate hooks up jumper cables to the portable generator and burns through the barred window, but it's too hot for her to slip through. MacGyver knocks out the guard and uses a discarded aerosol can to cool down the bars so she can escape. As they drive after Larkin, Kate blames herself and MacGyver tells her it could have happened to anyone. The girl admits that MacGyver's the first real friend she's had.
They lose Larkin's trail, but MacGyver figures that Hatcher must be keeping in contact with his lieutenant via radio. Working together, Kate and MacGyver build a triangulation device out of the Jeep's radio, her portable radio, and the Jeep's antenna. Since her radio's batteries are dead, MacGyver hooks wires up to a cactus to power it long enough for them to get a fix. They listen in as Hatcher tells Larkin to fire on the Clinton Narrows Bridge. MacGyver realizes that there's a marathon running that day and thousands of people will be killed.
They locate Larkin's position through triangulation. He's in the middle of an open field and armed with a shotgun. Unable to approach the missile launcher, MacGyver comes up with a plan. He uses the parabolic mirror from the headlight to build a crude solar collector, focus the energy through binocular lens, and direct it with a rear-view mirror. He and Kate put the device together and focus the beam of sunlight on Larkin's shotgun. The shells explode, setting off the nearby gas tank and knocking out Larkin and his men.
Hatcher calls to confirm the launch, and MacGyver tries to bluff, pretending he's Larkin. The arms dealer sees through his ruse and prepares to launch his missile at the bridge. Kate quickly reprograms the first missile to intercept the second one and destroy it.
Later, MacGyver meets with Kate at a club and tells her that the authorities have captured Hatcher. They're interested in recruiting her after graduation and will provide her with her own laboratory. Kate, who has dressed in more feminine clothing and has a date with a boy from her class, thanks MacGyver for all of his help. He promises that she'll see him again.