MacGyver gets up early to go fishing and stops for gas. He drives over a broken beer bottle and ends up having to put on a spare tire.
Elaine Harryman, an expectant mother, goes to the halfway house that she and her husband manage. She goes through his files and pulls one out, and then puts it in a briefcase. Her husband Andrew arrives and the ex-cons in the kitchen tell him that his wife has been there all night. Andrew goes in to see her and tries to comfort her, but she tells him that she knows all about how he's been using her. The files show that he forged papers to get ex-convicts from a prison gang onto the house's membership list, and then used them to create a small criminal empire for himself smuggling drugs and weapons. Andrew notes she can't be called upon to testify but she assures him she plans to tell the authorities everything. When he warns that she's implicated as well, Elaine tells him she doesn't care. As she starts to leave, he tries to stab her with a letter opener. She knocks it out of his hands and then hits him in the head when he kneels to grab it. Elaine runs out of the house, forgetting to take the car keys. As she runs down the street, Andrew tells his men Karl and Eric to go after her while his other man Mitch gathers the other ex-cons.
Elaine runs to the gas station as MacGyver finishes putting on the spare tire. She asks him for help and he gets her in and drives away as Karl and Eric drive up. A chase ensues and MacGyver pulls into an abandoned boat-manufacturing factory. MacGyver blocks the road behind them with a boat hull and their pursuers slam into it. MacGyver tries to drive away down the alley only to discover a boat hull at the other end is blocking their escape.
Eric and Karl call Harryman and tell him where they are. Meanwhile, MacGyver drives inside the factory and locks the doors behind him. They drive over a pit channel via a ramp but the ramp collapses, dumping the jeep into the channel. MacGyver and Elaine have no choice but to proceed on foot as Eric and Karl break in and come after them. As they seek refuge, Elaine explains she's a social worker and met Andrew in prison. He claimed he shared her dreaming of setting up a halfway home for ex-convicts. Their pursuers close in and MacGyver knocks out Eric with a blast from a water pipe, and then ambushes Karl.
After MacGyver ties up the ex-convicts, he returns to Elaine, who tells him that her water broke. She plans to give up the baby once she gives birth, given that it's Andrew's child and she considers it tainted. When she says that the baby kicks and MacGyver suggests it might be trying to tell her something.
Andrew sends Mitch to gather up the other ex-cons and head for the factory. Meanwhile, Elaine is starting to lose hope and warns that her labor pains are erratic. MacGyver tells her that the baby is counting on her and Elaine says she has no one else to count on since she's a black sheep in her family. MacGyver points out her and the baby are in the same boat. They manage to get the jeep turned around in the channel and drive it to the far end. MacGyver rigs some boards into a ramp so they can drive out and get back on the factory floor. They find an outside exit but Andrew arrives in his sportscar and starts shooting. MacGyver closes the door and drives off and Andrew comes after them. MacGyver drives into a freight elevator and sends it to the second floor, and Andrew has no choice but to find a flight of stairs and go up on foot. As he searches, he finds Eric and Karl and releases them.
On the second floor, MacGyver pulls out onto an outside ledge and finds a crane equipped with a freight platform and straps. He straps the jeep to the platform and then uses the remote to lower them down to the floor. However, the only way down is into the same blocked alley they were trapped in earlier. As Mitch and the others arrive, MacGyver drives back inside the factory and out the other side, crashing through a window. He drives into a scrapyard and camouflages the jeep, temporarily avoiding Andrew and his men as they drive by,. However, he realizes that they'll soon catch up and realize they've passed the jeep.
MacGyver hides Elaine and the jeep. She feels depressed at Andrew using her and MacGyver assures her that she's too good for him. As he prepares to leave, he spots Eric searching on foot. Using his fishing rod, MacGyver throws a sinker, hitting Eric in the head and knocking him out. MacGyver then goes to the boats outside the factory and finds a pack of signal flags. He then takes the bag used to hold the sail, and then finds tanks full of helium. Soaking the bag in water gives it enough surface tension to hold the helium in. Karl comes by and MacGyver tries the same trick with the fishing rod, but tangles the line on a mast. He yells to Karl and then yanks the mast into his head, knocking him out.
As the bag with the flags floats into the air, Mitch spots it and goes in pursuit. MacGyver uses his fishing line to rig a trap across a door and yank Mitch off his motorcycle. Two nearby policemen spot the flags and one recognizes it as a SOS. Meanwhile, Andrew has found Elaine and prepares to shoot her. MacGyver gets underneath the jeep and yanks Andrew under, and then punches him unconscious. Elaine tells him the baby is on the way.
Later, the paramedics and police arrive. While Andrew and his men are taken away, MacGyver gets to meet the new mother… and her daughter. MacGyver assures Elaine that they'll both be fine and Elaine decides to keep the baby.