MacGyver goes to a funeral home to attend the service for a good friend: Jack Dalton. However, as MacGyver regrets not having had a chance to thank Jack for saving his life, he notices that Jack's left eye is twitching. He quickly closes he coffin lid and gets the few mourners out, then locks the doors and demands to know what's going on. Jack warns him that if he gets out of the coffin, he'll end up dead for real, and MacGyver needs to get out. When MacGyver refuses, Jack explains that he's working undercover for the CIA. However, the other side blew his cover. Two men in suits try to get in, and Jack and MacGyver duck out the back, and then take off in Jack's messenger service motorcycle, complete with sidecar. The two men pursue in their car but MacGyver tells Jack to go down an alleyway, and then pulls the pin on the sidecar. The motorcycle and sidecar go through separately, but the pursuing car is unable to follow.
Jack goes to his "corporate headquarters" in a basement and explains to MacGyver how he faked his death in Central America. Thanks to a sudden updraft he managed to safely land and prepared to die. However, he got the dark spot on his x-ray checked and learned that it had disappeared. Deciding to turn over a new leaf, Jack went straight and started up the messenger service. However, he ended up running packages for the other side. The CIA contacted Jack and asked him to work undercover. Only Jack's contact, Light, and Light's partner knew who he was working for. They go to see Light at Jack's standard rendezvous, a road in the middle of nowhere. However, they discover Light, dead, and the CIA and police investigating. The agent in charge, Jay Michaels, spots them and immediately accuses them of Light's murder. Jack and MacGyver have no choice but to escape. Once they're gone, Michaels tells his partner to tell Mr. Berrenger that they have the situation under control.
Once the guys escape the police, MacGyver suggests they go somewhere and call Pete. Jack warns him that the CIA knows where he lives and works so they make a phone call. Pete is out of the country and his temporarily fill-in, Brockman, suggests they meet with the CIA to clear their names. However, when they arrive at the rendezvous spot that night, Michaels and his man are waiting for them. Jack and MacGyver figure Michaels is the double agent that Light was investigating. MacGyver throttles the motorcycle and knocks them down long enough for him and Jack to escape. Michaels tells his partner to tell Berrenger there's been a change in plans, and he'll make the delivery the next day. He figures that Jack and MacGyver will head for the spot where Jack made the drops.
Jack explains to MacGyver that Light's partner Shadow is the only person who can help them. They go to the club where she works as a dancer and where Jack made his drops. A messenger arrives with the last package, and Jack easily gets it to him. Shadow comes to their table and warns them that she has no one to turn to after Michaels killed her partner. The agents from the funeral home arrive and order them all out at gunpoint so they can murder them in the back alley. A dancer grabs one of the agents and MacGyver takes advantage of the distraction to get to the back with Jack and Shadow. As Jack and Shadow try to break down the exit door, MacGyver rigs a stage cannon with face powder and fires it at the agents when they come in. MacGyver and Jack try to capture the agents, who escape. However, Jack manages to pull off one of the men's shoes. It has a label stuck to it belonging to Berrenger Import/Export. Figuring that's where they can find Michaels, the trio head out. They get to Berrenger's shipping yard and spot Michaels going in. Shadow confirms that he's the leak in the CIA. He's carrying a briefcase and Shadow insists that it must contain the evidence they need to clear themselves.
Michaels meets with Berrenger and turns over the stolen equipment: a top-secret cypher machine. MacGyver slips into the yard inside of a crate, which is placed in the room where Berrenger is showing Michaels how he'll smuggle the cipher machine out of the country in the false bottom of a crate. Once they're gone, MacGyver exits the crate and lets Jack and Shadow in. They remove the cipher machine but Berrenger and his men get the drop on them. They force the trio into a garbage truck and Michaels has his men drive to a secluded spot and drop them off.
En route, Michaels' men decide to eliminate their prisoners early and activate the hydraulic sledge. When they're unable to stop the sledge with bracing, MacGyver uses a discarded piece of metal to get at the hydraulic controls. However, he activates the rear door, opening it. The sledge pushes them out and they have no choice but to leap for the door and hang on. The agents notice the trail of debris and pull over, then go back and investigate. MacGyver, Jack, and Shadow get the drop on them and knock them out.
The trio drives back in the garbage truck, doing everything they can to attract police attention. Berrenger is completing the sale to his Asian buyer when the garbage truck plows through the gate with the police right behind them. Jack and MacGyver capture Berrenger and Michaels, and Shadow identifies herself to the police.
Later, Jack notes that MacGyver owes him one and says that he plans to take up an honest career now that they've dealt with the CIA leak. All he has to do is pick up a mysterious package from a one-legged man…