An insurance investigator friend of MacGyver's is killed by a diamond thief with diplomatic immunity. Nikki Carpenter, the friend's sister, is teamed up with Macgyver against his wishes to get the diplomat deported.
MacGyver goes to a small town in Arkansas to bail Jack Dalton out of another predicament. MacGyver ends up getting arrested along with Jack and sent to a prison camp where there are forced to dig in an abandoned mine for hidden millions of dollars.
When a satellite carrying a genetic experiment crashes to earth MacGyver is sent in to recover it. When he arrives he discovers that the experiment mutated in space and now ages animals at a vast rate. It is taken back to the lab but the scientist in charge doesn't want to destroy it.
MacGyver's boss Pete oversees the disarming of a nuclear warhead. A deadly explosion at the disarming facility causes Pete to accept full responsibility and retire from the Phoenix Foundation. However, MacGyver soon suspects that the replacement for Pete is responsible for sabotaging the warhead.
MacGyver agrees to accompany Jack on a flight to bring a rich woman and her recently acquired jewels to France. However, as soon as they land in France they are arrested for theft and regardless of their pleas, accused of complicity.
When MacGyver's research into the wildlife around the planned building site of a marina threatens to cause a shutdown of the project, the owner hires a beautiful woman to persuade MacGyver to change his mind... by any means necessary.
Jack Dalton and MacGyver suddenly become dads when a baby is left in Jack's airplane hangar. They search for the mother of the baby, who used to be a girlfriend of Jack's, and thus there is the possibility that Jack is the baby's father.