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.
In the middle of nowhere, MacGyver gets involved in a car accident. He is luckily found by an Amish family and nursed back to health. MacGyver then helps the Amish community to confront a construction crew that is trying to force them off their land.