In East Berlin, pallbearers carry a coffin containing MacGyver. They drive him to the border checkpoint where three “mourners” are waiting for the coffin. The guards remove the coffin and put it on the bridge, then call over the mourners to collect it. They carry it toward the West Berlin side of the checkpoint, but the head soldier gets a phone call. He orders them to stop the coffin and the mourners run to the side and throw the coffin into the river below. MacGyver triggers a device which blows the coffin apart, revealing a compact jet ski. He rides it to safety as the guards fruitlessly shoot at him.
A foreign agent, Quayle, reports to his superiors about MacGyver, the only blemish on his career. Quayle assures them that he’s ready for MacGyver and has plans to prevent the intelligence MacGyver smuggled out from reaching American Intelligence. They warn that this is his last chance and authorize his mission.
MacGyver arrives by helicopter in downtown Los Angeles and several foreign agents move in. A woman, Karen Blake, arrives and claims to be his girlfriend, while telling him that the men are closing in. She gets him away to meet with Pete Thornton at a special safehouse: an expensive manor. As they arrive, Quayle is in the control room and has security cameras monitoring their every movement. They go in through the gates and meet with Pete Thornton, MacGyver’s old friend. They talk briefly about old times and MacGyver reveals he has the stolen microfilm. Pete reveals they have a leak in departmental security and is handling the matter privately without his office’s knowledge.
Pete takes them into a trophy room and introduces them to Mrs. Chung, a cryptologist who will be reviewing the data. Pete tells Karen they’ll all be staying. Mrs. Chung shows them the computer, which comes on in its own. Quayle announces himself on the loudspeaker and then detonates the computer remotely. With another button he seals all the windows and doors. When Mrs. Chung tries to open an inside door, she triggers a poison needle that knocks her unconscious. Quayle comes on a monitor and MacGyver explains he’s a double agent who he defeated. Quayle plans to destroy the microfilm and MacGyver. The phone lines are sabotaged and Quayle dares them to escape.
MacGyver, Pete, and Karen head upstairs and discover that Karen’s car is gone. Quayle activates remote motion-sensor guns while Pete and MacGyver figure the gate is booby trapped. MacGyver opens the door and nothing happens, so he takes a suit of armor and slides it outside. the guns make short work of it. They pick up the pieces and gather them in a blanket. They go to the kitchen while Quayle reseals the door. MacGyver and Pete keep a conversation going complimenting Quayle while MacGyver attaches a metal bowl to a blender and creates a makeshift jamming device to jam the cameras. Pete realizes his radio phone is in his briefcase in the library and they split up to keep Quayle guessing.
Quayle spots Pete heading for the trophy room. In the kitchen, Karen talks about her childhood dreams of being a spy. Pete gets to his briefcase and tries to call out, only to discover that Quayle has tapped into the line. He sets off an electrical charge rendering Pete unconscious. Karen prepares to go out next and MacGyver gives her a kiss for luck. Once she’s gone, MacGyver builds a crude motor out of batteries, a hand mixer, and rubber bands, and attaches it to a cart. He’s unaware that Karen has gone to see Quayle: she’s the security leak. She’s worried that MacGyver will figure things out and Quayle is prolonging things. He points out she needs to worry about someone close to him, and tells her to find out exactly what MacGyver is doing. He gives her a portable radio to stay in touch and then lets her out.
Karen goes to a room next to the kitchen where MacGyver has taped the armor back together and wired it to the cart. She watches him through a peephole and tells Quayle he’s going out of the back door. Quayle reassures her he only plans to embarrass MacGyver for the moment, but she’s not reassured. MacGyver gets the back door open and sends the cart out behind a hedge. The automatic guns open fire and MacGyver crawls along the ground behind it. He shoves the cart in one direction and dives over the hedges and off the grounds in the other direction. Quayle gets on the loudspeaker and tells him to return or he’ll kill Pete. He turns off the guns so MacGyver can come back in and MacGyver has no choice but to return.
Quayle notes that Karen is showing undue concern but she tells him she’s been ordered to recover the microfilm, not toy with MacGyver. He tells her to go to the trophy room and get the microfilm, and that Pete has been shocked. She and MacGyver arrive and find Pete unconscious, and says that he’s been electrocuted. Karen thanks MacGyver for coming back and they make Pete comfortable then go back to the kitchen. MacGyver figures the main power line is in the basement and if they cut it off then Quayle loses his edge. MacGyver grabs some kitchen supplies and then hugs Karen… and takes the radio receiver. He points out that he knew she was a double agent when the hit men at the helipad didn’t try to kill him, and she immediately knew Pete was electrocuted. She explains that Quayle and his superiors have her brother, who works for the company. He asks her to help him capture Quayle to use as a bargaining chip, and if that fails he promises to rescue her brother personally.
Karen agrees to help and takes his supplies with them. Quayle spots them and activates internal guns that close in. MacGyver mixes vinegar and baking soda into an urn, creating a smoke screen. Karen guides him to the hidden panel leading to Quayle’s lair. She warns that the door to the security center is sealed and Quayle is armed. MacGyver figures that Quayle will come out when they cut off the electricity and scatters some duct piping across the hallway. Inside the power room, MacGyver rewires the panel while Karen scatters junk around the room so there’s only one way for Quayle to come in, then finds a mirror and makes a periscope. Finally he rigs a water pipe to fire water on command into the exposed wiring.
With everything ready to go, MacGyver cuts the power. Quayle grabs a gun and goes to investigate, while Karen kisses MacGyver for real. When they hear Quayle approaching, they hide and watch via the periscope as Quayle comes in. However, the mirror is out of position and Karen reaches up to adjust it. Quayle spots her and opens fire. Karen comes out and claims she was trying to help him. She shoves him toward the paneling and MacGyver releases the water, shocking the villain long enough for MacGyver to punch him unconscious.
Later, Pete informs his superiors what happened while a confused Mrs. Chung wakes up and MacGyver assures her that everything’s taken care of.