Jack and MacGyver are flying back from Mexico in the plane that Jack bought at a drug enforcement auction. Both engines cut out and the plane starts to go down. Jack tries to lower the landing gear, but only one wheel goes down. MacGyver grabs the one parachute and climbs down onto the stalled landing gear. He spots the leaking hydraulic fluid tube and grabs a fire extinguisher. MacGyver's plan works... and the wheel drops, dropping him as well. As Jack brings the plane into land, MacGyver loses his grip and falls, and activates his parachute to come in for a landing. As Jack coasts to his hangar, MacGyver gets there and promises he never plans to fly again. He leaves despite Jack's pleading.
At the Officers Club, a bar for pilots, the owner Cutler is on the phone negotiating with Milland, who wants $20,000 in real money for the currency paper, rather than the $100,000 in counterfeit bills that Cutler is making. Cutler's henchman Durst notices bills lying on the floor and Cutler admits he put the counterfeit samples in the poker chip dryer to age the bills. The rest of the counterfeit money is gone and Cutler realizes that the plates are gone as well. In the bar, a waitress, Katie, goes in the back to check on her baby boy. Her boyfriend Carlo reveals they're leaving town thanks to the money he's stolen from Cutler. Cutler easily figures out Carlo is involved and they go to talk to Katie. Carlo heads for the alley but Durst and Cutler chase after him. Durst shoots him down despite Cutler's protestations. Katie sees the shooting and leaves with her baby, as Cutler sends Durst to get her. Cutler searches Carlo's bags and realizes that there are no plates, and figures that Katie can't get far.
MacGyver is sleeping at his houseboat when Jack arrives with a new opportunity: his first air shipping contract. Jack needs him to repair the plane. MacGyver doesn't want to help until he realizes the alternative is letting Jack stay with him when he gets kicked out of the hanger. They go back to the hanger and discover the door is unlocked. They hear a baby crying and discover that someone left the baby boy in the cockpit of the airplane. They're unaware that Katie is watching from the door. She slips away while they try to figure out who the baby is. As they take it outside, they find a note from Katie saying it's Jack Jr. Jack starts to call Social Services and denies he's never heard of any Katie, but his eye twitches and he admits that he met her at the Officers Club. MacGyver gives him the baby and goes to find a policeman. However, Jack panics and calls him back when he discovers the baby needs a diaper change. Jack searches his bundle for diapers and finds bundles of cash.
Katie goes to the apartment of her friend Dawn, who warns that Cutler and Durst have already been there. Dawn gives her money for a ticket out of town and tells her she needs to leave.
At MacGyver's houseboat, Jack is less than willing to embrace fatherhood as the baby cries incessantly. MacGyver gives the baby to Jack to hold, and he promptly dozes off. The baby knocks a lamp over, spilling beer onto a computer keyboard. MacGyver tells Jack they're not going to touch the $95,000, and figures it's crooked. Jack knows about Carlo, who Katie dumped Jack for. Jack prepares to go back to the hangar to get his plane going. However, as they pick up the blankets, the metal counterfeit plates fall out. The next morning they take the plates and the money to Pete, who confirms that it's counterfeiting. The plates are real: someone working on the inside of a mint stole currency plates. Pete is less than thrilled to see that MacGyver used duct tape to fasten Jack Jr.'s diaper. He takes over and MacGyver and Jack leaves the baby with him and make a hasty exit to check out the Officers Club.
Jack and MacGyver talk to Dawn, who works at the club, and try to get answers from her. Durst notices them and recognizes Jack as the guy who used to go with Katie. Jack gives Dawn his address to pass on to Katie. Once they leave, Durst calls her up to their office.
At the hanger, Jack is bonding with Jack Jr. while Pete tells MacGyver that the police found Carlo's corpse. As he leaves, MacGyver finishes working on a RC airplane and Jack tells him that he's willing to take care of the baby until they get things resolved. He asks MacGyver to help him get the plane fixed so he can make the money to support Jack Jr. Outside, Cutler and Durst arrive and come in, armed and wearing mask. They demand to know where Katie is, but when MacGyver admits they don't know where Katie is, the men prepare to take the baby. MacGyver activates the RC plane, distracting the men while Jack starts up the plane. MacGyver crashes the RC plane into a control panel and then sprays the men with high-pressure water to hold them at bay. He tells Jack to radio the police and Cutler and Durst run for it.
Back at the Phoenix Foundation, Pete thinks the baby should be turned over to Social Services but Jack doesn't want to give up the baby. The Federal authorities have had no luck finding Katie, and MacGyver tries to figure what she's thinking. He figures she would have holed up in a hotel somewhere but she has no way to contact Jack. So they fly a sky banner telling her whom to call. Meanwhile, Milland meet with Durst and Cutler to deliver the currency paper. They give him paper and then gun him down.
Katie sees a news story on Jack and MacGyver's sky banner scheme.
Jack and MacGyver wait at the houseboat and Jack is still concerned about getting his plane working. Jack Jr. starts to cry and Jack takes over. Surprisingly, he manages to entertain the baby and MacGyver realizes he's getting into it. MacGyver admits he's considered a family and son before but never committed himself. Katie calls and arranges for them to meet her. They get to the rendezvous spot with Jack Jr. and Katie embraces her son. They take her back to the houseboat where Pete learns that the police found Milland and the bullet matches with the one in Carlo. Milland worked for a paper manufacturing company that makes stock for the government. Federal agents are going to the Officers Club and Pete and MacGyver go to join them. Jack wants to talk about the baby but Katie asks to freshen up first. She leaves Jack Jr. with Jack and goes upstairs.
The authorities arrive at the Officers Club and break in. Durst and Cutler go into the hidden chamber with the counterfeit printing press and wait the intruders out.
Jack is reading to Jack Jr. as Katie comes down and sees how well he's doing. She thanks him for his help but finally admits that the child is Carlo's, not Jack's. She named him after Jack because of all his good qualities. A disappointed Jack hands the baby over to her and admits he's never had any luck with keeping anything.
Pete and MacGyver arrive at the club and realize the Treasury agents haven't found anything. Durst and Cutler watch them through a two-way mirror and listen as MacGyver gives Jack a call. However, as the Treasury agents leave, MacGyver realizes that the club dimensions don't match. Durst aims a shotgun at him as MacGyver studies the mirror. MacGyver then turns off the light, revealing the lit chamber on the other side. MacGyver pulls Pete down behind a couch, and then uses it as a battering ram to knock Cutler and Durst off a balcony to the club floor below.
At the houseboat, Katie is preparing to leave as Pete, Jack, and MacGyver look on. Jack offers to take Katie to dinner and get her to stay, and Pete and MacGyver are eager to take care of the baby. MacGyver is eager to start Jack Jr. on a hockey career..