Abe Sherman is working as a temp security guard at Harding Aeronautics. He breaks into the company's hangar using a security card, puts the top secret set of blueprints for a stealth helicopter in a flight bag, and then steals the helicopter itself. As he leaves, the head of security, Elliott, and his two assistants Major Sneed and LaManna come running up. They can't shoot at the helicopter for fear of damaging it, but quickly realize that Abe is the person responsible for the theft. They have the control tower track the helicopter.
MacGyver meets with his friend, Philip Sherman, who is preparing for his son Jeff's bar mitzvah. Jeff is MacGyver's godson and MacGyver is there to help. Philip asks MacGyver to make sure that his father Abe, a tuba salesman, gets there. Jeff has called the bus company to confirm that Abe is on their way. MacGyver agrees to pick up Abe when the bus arrives in town and get him to the ceremony.
Abe arrives in town and wonder who MacGyver is. He finally remembers that MacGyver is his son Philip's friend from college and asks MacGyver to pick up his present for Jeff at the post office. MacGyver goes inside to get it, unaware that LaManna and Major Sneed are watching the building. When MacGyver leaves, they track the package via a radio transmitter and LaManna draws his gun. He tells MacGyver to hand over the package, saying it's a flight bag. Abe drives up and MacGyver leaps in so they can make their escape. LaManna fires at them and MacGyver demands to know what's going on. Abe claims the package contains sheet music and the shooter is a rival tuba salesman. MacGyver isn't convinced and points out that Abe said it was a present for Jeff.
They pull over and Abe finally admits that it's complicated. He explains he's working for the CIA and needed to steal the helicopter from Harding Aeronautics. However, he's persona non grata with the CIA so they'll disavow him if he gets caught. MacGyver insists that they need to go to the authorities and Abe reluctantly agrees. Meanwhile, Elliott and his men convince the deputy sheriff that they're with the FBI and they need his help finding Abe. Harding contacts them to tell them to kill Abe when they find him.
MacGyver stops at an intersection and Abe grabs the keys. He explains that he needs the helicopter to bring Marcel Perigot, the President of San Rochelle, to justice. Abe planned to take the helicopter to Perigot as a gift, then abduct the dictator and return him to the States. MacGyver convinces Abe to take the stealth helicopter to the Phoenix Foundation for safekeeping and then go to the bar mitzvah.
Abe takes MacGyver to the stealth helicopter, camouflaged in the woods. His security card doesn't work, but MacGyver reads the manual and realizes that it can be remotely controlled by a laser beam. He uses a mirror to reflect sunlight and trigger the sensor to open the door. However, as they fly to the Foundation, Abe uses a hidden canister of knockout gas to render MacGyver unconscious.
The next morning, MacGyver discovers that Abe has flown the helicopter to San Rochelle. Abe explains that as a CIA agent he helped put Perigot in power and wants to make amends by capturing Perigot and bringing him back for trail. He needs the helicopter because Harding made two prototypes: one for the Defense department and the other to sell illegally.
Abe lands the helicopter at a town in San Rochelle near Perigot's manor. The dictator's soldiers take them to see Perigot, who is amusing himself performing magic tracks. Abe offers to sell Perigot the helicopter after a test flight but the dictator wants it immediately. Abe convinces him to go for the flight and he gets in with his lieutenant, Fritz. However, as Abe prepares to gas Perigot unconscious and return him to the States, Elliott, LaManna, and Major Sneed arrive and identify Abe as an ex-CIA agent who stole the helicopter. Perigot has his men arrest Abe and MacGyver and orders their execution by hanging.
Perigot's soldiers lock MacGyver and Abe in the storeroom of a monastery. Meanwhile, Elliott contacts his superiors and discovers that MacGyver is actually a Foundation agent. He explains to LaManna that he actually is a FBI agent working undercover and he has new orders to get MacGyver and Abe to safety. LaManna admits that he's an undercover agent for the Office of Budget and Management, investigating Harding's illegal sales of the stealth helicopter. Elliott explains that Abe is still a CIA agent working deep-cover to bring Perigot back for trial. LaManna goes to get some gasoline to start a fire and create a distraction while Elliott goes to capture Major Sneed and Perigot.
While Abe admits that he's been a lousy father and grandfather, MacGyver gets alcohol from a wine cask and uses a bellows to spray it through the keyhole of the door and create a mist of alcohol on the other side. He then makes a fuse out of string and wax and makes a spark using the hoop of a stove. The alcohol ignites, blowing the door open. However, the explosion distracts LaManna, who drops his cigarette on the gas can and that explosion knocks him out. Elliott tries to arrest Sneed and Perigot but they get the drop on him when MacGyver's explosion goes off. Abe and MacGyver get to the helicopter but Fritz is waiting inside and recaptures them.
The four prisoners are taken to the gallows to be hanged. Playing on Perigot's vanity, MacGyver asks for a shave as his dying request. Perigot loans him his personal mirror and MacGyver reflects sunlight to trigger the weapon systems on the nearby helicopter. He activates the knockout gas dispersal system and holds his breath. Abe does the same and everyone else is knocked out. They pick up Perigot, Elliott, and LaManna and fly away in the helicopter.
Later, Philip and Jeff are at the synagogue and prepare to go in for the ceremony. Abe hasn't shown up and Philip figures that his father isn't going to show. MacGyver arrives with Abe just in time and Jeff asks where they were. When Abe claims he was on tuba sales business, his son asks him to tell the truth for once. Abe turns to MacGyver, who admits that it's kind of complicated.