Jack Dalton has bought a plane cheap at a drug enforcement auction and is flying it back from Mexico with MacGyver in tow. The engines go out and the plane starts to go down as they approach the airfield. One landing gear wheel refuses to go down and MacGyver grabs a parachute and climbs down to fix it. He discovers the hydraulic fluid has leaked out and uses a fire extinguisher to supply the pressure. It immediately drops and MacGyver falls out, barely holding on. He finally loses his grip and plummets toward the ground, and uses his parachute to come to a safe landing. He gets to the hangar as Jack pulls in and informs his friend he's never flying with him again.
At a pilots' bar named the Officer's Club, the owner Cutler has just finished negotiating by phone with Milland. Milland is breaking their deal, asking for $20,000 in real money for the currency paper he's selling Cutler, rather than $100,00 in counterfeits. Cutler's partner Durst notices counterfeit bills lying on the floor and they realize someone has stolen the first batch they printed. Worse, the plates are gone as well.
In the bar, a waitress, Katie, checks on her baby boy. Her boyfriend Carlo comes in and says that he's leaving town and wants her to go with him. He explains that he stole money from Cutler to finance their trip. Up in the office, Cutler and Durst realize Carlo has been snooping around and go to find Katie. They spot him and chase him out into the alley. When he tries to escape by climbing a fence, Durst shoots and kills him. Katie sees them kill her boyfriend and flees with her baby. Durst goes after her while Cutler searches Carlo and realizes the money and the plates are gone. Katie escapes but Cutler tells Durst that she can't get far.
Jack visits MacGyver at his houseboat and says he's got a new contract: shipping porta-potties to Panama. All he needs is MacGyver's help to get the plane working. MacGyver isn't interested until Jack points out that the alternative is his staying with MacGyver when he runs out of money. MacGyver quickly volunteers to help and they go back to the hangar. They hear crying and discover that someone has left a baby in the cockpit of Jack's plane. As they check on it, Katie slips out the side door. They find a note from Katie saying that the boy's name is Jack Jr. Jack isn't interested in keeping the baby and starts calling Social Services. MacGyver quickly determines that he does know a Katie and goes to call the police. However, Jack panics when the baby needs a diaper change and calls MacGyver back. However, Jack cheers up when he realizes there's $95,000 wrapped in with the baby.
Katie goes to see her friend Dawn, who tells her that Cutler and Durst have been there looking for her. Dawn won't let her stay but gives Katie enough money to get out of town.
MacGyver and Jack take Jack Jr. back to the houseboat and try to make him comfortable. It soon becomes clear neither is ready for fatherhood. Jack wants to keep the baby, and the $95,000, but MacGyver figures it's tied up with something crooked. As Jack heads back for the hangar, the metal counterfeiting plates fall out of the baby's blankets. They take the plates and money to Pete Thornton, who confirms it's involved with some kind of counterfeiting scheme. The money plates are real: they have a report that someone working at a mint stole them. He agrees to take care of Jack Jr. while MacGyver and Jack go to the Officer's Club. They talk to Dawn, who refuses to say anything about her friend. She agrees to pass on Jack's phone number if she sees Katie. Cutler and Durst are in the upstairs office and see Jack, and recognize him as her former boyfriend. Once MacGyver and Jack are gone, Durst calls Dawn up to the office.
At the hangar, Jack is playing with Jack Jr. while Pete lets MacGyver know that the police found Carlo's corpse. He heads back to the office while MacGyver finishes working on a RC airplane. Jack is now eager to take care of Jack Jr. and asks for MacGyver's help to get the plane working so he can make the Panama delivery and have enough money to raise Jack Jr. Cutler and Durst show up, wielding shotguns, and demand to know where Katie is. When MacGyver admits he doesn't know, the men prepare to take the baby. MacGyver sends the RC plane after them and buys enough time to get to a water hose and spray them down. He tells Jack to call the police on the plane radio and the crooks take off.
Jack and MacGyver check in with Pete, who insists they should turn Jack Jr. over to Social Services. Jack no longer wants to. With no way to contact Katie, they decide to fly a sky message across the city with a phone number for her to contact them.
Cutler and Durst meet with Milland on a deserted stretch of road and get the authentic currency paper. However, once they have the paper they kill him.
Katie is on the streets and sees a television newscast about the sky banner.
MacGyver and Jack wait at MacGyver's houseboat and Jack keeps Jack Jr. entertained. MacGyver admits that he's often thought about having a family but never made the commitment. Katie calls and sets up a meeting. They pick her up and get her back to the houseboat. Pete meets them there and informs them that Milland has turned up dead, killed with the same gun that was used on Carlo. Milland was an employee at a paper manufacturing company that produced currency paper for the government. The Treasury Department has traced the counterfeiting to Cutler and Durst at the club and MacGyver and Pete go to help search the place.
At the club, Cutler and Durst hide in a secret counterfeit manufacturing room in the upstairs office as the Treasury agents break into the club and search the place. The crooks watch everything through a two-way mirror.
At the houseboat, Katie finally admits that Jack Jr. is Carlo's son, not Jack's. She named the baby Jack Jr. because of the time they were together and all the good qualities that Jack had. A disappointed Jack hands over the baby.
MacGyver and Pete arrive at the club and check out the upstairs office as the Treasury agents leave. MacGyver notices that the upstairs dimensions don't match the downstairs floorplan and there's extra space upstairs. He turns off the lights, revealing Cutler and Durst on the other side. MacGyver drags Pete to cover behind a couch as Durst opens fire, and then they use the couch to shove both crooks through the window to the floor below.
Later, Katie is at the houseboat preparing to leave. She isn't sure where she's going and Jack convinces her to stick around so he can show her the city. MacGyver and Pete volunteer to look after Jack Jr., and are soon teaching him how to play hockey…