MacGyver goes to a funeral home to pay his respects for... Jack Dalton. MacGyver looks down at his friend's body and remembers how he would get into trouble. He regrets not having a chance to thank Jack for saving his life. However, MacGyver notices that Jack's left eye is twitching and quickly slams the lid down. He asks the few mourners to leave. Once everyone is out, MacGyver opens the lid and Jack opens his eyes. He warns that if he gets out of the coffin, he may end up dead for real. Jack tells MacGyver to leave. Outside, two men in suits get out of a car and enter the funeral home.
MacGyver demands answers and Jack explains that he's working undercover for the CIA, and the other side blew his cover. The two men try to get in and Jack and MacGyver flee out the back. Jack drives them away on a motorcycle with sidecar and the two agents give pursuit. He explains that he's running a messenger service but was hired to deliver top-secret government documents to who turned out to be the other side. The CIA then contacted him and asked him to keep making deliveries until they could track the inside leak. The agents close in and MacGyver tells Jack to drive down an alleyway. MacGyver pulls the pin on the sidecar and slips through the gap, and Jack follows him. The agents are unable to pursue.
Jack drives to his new "corporate headquarters" and enters through a sidewalk-loading elevator. He explains he managed to fake his death in Central America, but was rescued thanks to a warm updraft. Jack explains that he crashed and figured that he had a month to die so it didn't matter where. However, the dark spot on his x-ray disappeared. Jack plans to turn over a new leaf and live honestly, and MacGyver suggests he go to the CIA. However, Jack warns that only his contact and the man's partner know that Jack is working for the CIA. Jack and MacGyver go to see Jack's contact, Light, at their standard meeting spot. However, the police are there and Light is dead. A CIA agent, Jay Michaels, accuses them of the murder and they quickly escape. The police give chase while Michaels tells his assistant to tell Mr. Berrenger that everything is under control.
Jack and MacGyver lose the police, but Jack warns that the CIA knows where MacGyver lives and works. They go to a payphone, and discover that they're wanted for murder. Pete's out of the country so his temporary replacement, Brockman, sets up a meeting for 10 o'clock that night. They go to the rendezvous spot and find Michaels and his partner waiting for them. He draws a gun on them, and MacGyver and Jack figure he's covering up that they're double agents. MacGyver sends the motorcycle at them, knocking them down long enough for them to escape. Michaels tells his partner to tell Berrenger there's been a change in plans, and Michaels will make the final delivery the next day. He figures that Jack and MacGyver are heading for the drop spot. Meanwhile, Jack tells MacGyver that Light's partner Shadow also knows about his arrangement, and she works at a dance club.
At the club, Jack explains that he used the place as a drop when he was working with Light. He doesn't see Shadow, but a messenger arrives with the last package. MacGyver suggests they get the package and use it for leverage. Jack easily gets the package and one of the dancers approaches them. It's Shadow, but she admits there's nothing she can do and the CIA killed her partner. The other side's agents arrive and force them to leave so they can dispose of them. As they go backstage, a dancer garbs one of the men and when he shoves her off, a fight breaks out. MacGyver, Jack and Shadow run to her dressing room, but the rear door is fully locked. As they struggle to get it open, MacGyver loads a prop cannon with face powder. He fires it at the agents when they come in blinding them. Realizing the men can prove their innocence, MacGyver and Jack try to capture them but they escape. Jack manages to grab one of the agents' shoes, and there's a label for Berrenger's Import/Export stuck to the sole. They figure the men work for Berrenger and Shadow gets them out before the police arrive.
The next morning, the trio arrives at Berrenger's warehouse and get through the fence. Michaels arrive with a briefcase and Shadow identifies him as the Company leak. She explains that she had no evidence against Michaels, but the briefcase may have what she needs. Michaels goes into the warehouse and meets with Berrenger. He prepares to hand over a cipher machine, and Berrenger explains he's prepared a special way to get it out of the country. Outside, MacGyver hides in a crate and the workers take it inside. Berrenger shows Michaels a hidden compartment in a crate used to ship a bronze statue. Berrenger's buyer arrives and MacGyver kicks his way out of the crate. He unlocks the door and lets Shadow in while Jack watches the door. MacGyver shows Shadow the hidden cipher machine, but Berrenger captures them before MacGyver can threaten to destroy the cipher machine. Jack tries to bluff their way out but one of Berrenger's agents gets the drop on him.
Berrenger's men force the trio into a garbage disposal truck and then activate the hydraulic press, sealing them in. The agents drive the truck off and activate the compactor en route. The trio tries to rig bracing to stop the sledge without success, so MacGyver uses a piece of metal to get at the controls. He activates the door instead but can't jump due to the fact they're moving at high speed. They leap onto the door and hold on, and the two agents notice the garbage spilling out. They pull over and go back to investigate. They find no one there, but MacGyver and Jack jump down from the top of the truck and attack them. With some help from Shadow, they knock out the two agents.
Back at the warehouse, Berrenger and Michaels complete the sale. As the trio drives back, Jack honks the horn and runs a red light to attract police attention as they head back to the warehouse. They arrive just as the buyer prepares to leave with the cipher machine. MacGyver tackles Michaels, Shadow identifies herself and subdues the buyer, and Jack captures Berrenger.
Later, Jack is leaving on his motorcycle and notes that now MacGyver owes him. Jack vows that he's going to commit to an honest day's work, but first he has to detour to the pier to pick up a package from a mysterious man with a peg leg. When MacGyver starts to panic, Jack explains that it's a joke.