Security guard Abe Sherman breaks into an office at Harding Aeronautics' airfield hangar using a stolen security card and removes a set of blueprints for the stealth helicopter stored there. He then goes out and uses an access card to get into the helicopter. He replaces the fire extinguisher inside the helicopter with a fake one he's been provided with and then flies away with it as the security teams run to investigate. The head of security, Elliott, tells his men LaManna and Major Sneed, not to fire for fear they'll damage the chopper. They quickly figure that their new temp security guard, Sherman, stole it, and call the tower to track it.
MacGyver stops at a store to meet the owner, Philip Sherman. MacGyver is the godfather of Philip's son Jeff, who is having his bar mitzvah the next day. Philip tells MacGyver that his father Abe, a tuba salesman has said he'll be at the ceremony but he isn't so sure he'll be there. MacGyver and Jeff insist he will and Jeff says that he called the bus company to confirm Abe was on the bus. However, he asks MacGyver to pick up Abe just to be on the safe side. MacGyver promises that he'll get Abe to the ceremony.
MacGyver meets Abe at the bus stop. Abe mistakes MacGyver for Philip at first. He asks MacGyver to take him to the post office to pick up Jeff's present. When they arrive, Abe spots LaManna waiting outside and asks MacGyver to get it. He finally recognizes MacGyver and knows he's been involved in espionage. MacGyver goes in past LaManna, who is in radio contact with Major Sneed in a nearby van. They track the bag and determine when it's moving, and that MacGyver has it. LaManna pulls a gun and demands the flight bag, and MacGyver has no idea what he's talking about. Abe drives up, sends LaManna flying, and has MacGyver get in so they can escape. MacGyver demands to know what's going on but Abe contains the package contains tuba music. When MacGyver points out Abe said earlier it was Jeff's present, Abe corrects himself and claims the people doing the shooting are rival tuba players.
MacGyver has Abe pull over and forces him to explain. He takes the keys and threatens to go to the sheriff. Abe finally admits that he works for the CIA and stole a stealth helicopter from Harding Aeronautics. MacGyver says he has to call his people and call the mission off, and Abe admits that he's persona non grata with the Company and what he's doing is illegal. MacGyver convinces him they need to go to the authorities and Abe agrees.
Elliott and his men pose as FBI agents and meet with Duke Luke, the deputy sheriff. With the sheriff gone, they convince Duke Luke to help them organize a search. They get word from Harding that they're to kill Abe.
When MacGyver stops at a stop sign, Abe takes the keys and insists he has to go through with the mission to bring Marcel Perigot, the President of San Rochelle, to justice. He's a major terrorist and there's a Federal warrant for his arrest. There's no extradition treaty with San Rochelle. Abe warns that he's in too deep and the CIA would disavow him. MacGyver suggests they fly the helicopter to the Phoenix Foundation and get to the bah mitzvah.
Abe takes MacGyver to the helicopter, hidden in the woods, but discovers his security card doesn't work any more. MacGyver goes over the technical manual and admits it's an impressive piece of machinery. There's an exterior laser sensor that can be used to activate the on-board computer. MacGyver uses a flashlight to gain access and Abe goes over the technical manual to learn how to activate the onboard weaponry.
As they fly for the Phoenix Foundation, Abe triggers the fake fire extinguisher he placed earlier and then puts on a helmet with an air mask. The fire extinguisher triggers knockout gas and Abe takes control as MacGyver passes out.
MacGyver wakes up the next morning and discovers Abe has flown the helicopter to San Rochelle. Abe admits he spearheaded the CIA operation to put Perigot in power. He plans to borrow the helicopter as bait to get close to Perigot. However, Harding produced two helicopters: one for the Defense Department and one to sell on the black market. Abe had to steal the helicopter to get to Perigot.
They land in the town square and soldiers promptly arrive to take them into custody. They're driven to Perigot's manor where he amuses himself with sleight of hand and demands to know what they've brought him. They take him to the helicopter and Abe gives his sales pitch. Perigot agrees immediately to buy it without Abe take him on a test flight so he can abduct the president. Abe convinces him to take a test flight. They get in along with Perigot's lieutenant and Abe and MacGyver put on their helmets with rebreathers. However, Elliott and his men arrive and Perigot tells Abe to shut it down so he can see what's going on. They confirm that Abe was booted out of the CIA six months ago and he's just a security guard that got greedy. Perigot has his men remove Abe and MacGyver from the helicopter and orders them to be hung shortly.
Perigot's men lock Abe and MacGyver into a storage room at an old monastery. While MacGyver looks for a way out, Abe admits that he wasn't much of a CIA agent or a father. Outside, Elliott contacts his superior and learns that MacGyver is actually a Phoenix Foundation agent. He tells LaManna that now they have to rescue MacGyver and Abe. Elliott reveals he's actual a FBI agent investigating Harding and Sneed for bilking the government. He offers LaManna immunity for help, but LaManna reveals he's an undercover agent for the Office of Budget and Management. They've been conducting an audit of Harding's operations. Elliott explains that Abe is a deep-cover agent with the CIA. He tells LaManna to create a distraction while he captures Sneed and Perigot and use them as hostages so they can all escape.
MacGyver opens a cask of old wine and drains out the resulting alcohol. He makes a fuse out of a string and wax and sticks it through the keyhole. Then he uses the billows to spray a cloud of alcohol in front of the door. Finally he then ignites the fuse and they duck for cover.
LaManna prepares to start a fire while Perigot performs more card tricks for Major Sneed. Elliott captures them at gunpoint just as the alcohol ignites, blowing open the monastery door. Startled, LaManna accidentally drops his cigarette on the tie he's using as a fuse, setting off the gasoline prematurely. When Elliott is distracted, Major Sneed captures him. MacGyver and Abe get to the helicopter only to discover Perigot's lieutenant Fritz waiting for them.
Abe, MacGyver, Elliott, and LaManna are tied up on a scaffold and Perigot prepares to dispose of them. MacGyver asks for a last request and Perigot let him have a shave. Major Sneed is suspicious but Perigot offers MacGyver an electric razor and a mirror. MacGyver reflects sunlight at the laser sensor on the nearby helicopter and activates the knockout gas dispersal unit. MacGyver and Abe hold their breaths as everyone else is knocked out. They get clear of the gas cloud and leave with Perigot and the two government agents.
Later, Jeff waits at the synagogue and Phillip warns that they won't show. As they start to go in, MacGyver and Abe pull up. Phillip thanks Abe for coming and they embrace. Jeff wonders what kept them and Abe starts to tell a tale of tuba salesmen. Phillip tells him to tell the truth for once and Abe turns it over to MacGyver. MacGyver has to admit it's kind of complicated.