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.

A mountain man who witnessed toxic waste dumping has testimony that is vital for MacGyver and Pete. But his flashbacks back to his time in Vietnam cause him to be unstable and may threaten their case.

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.

MacGyver's friend Penny Parker gets the lead part in a new musical. MacGyver suspects it may be a set up by his arch-nemesis to trap him.

The young son of MacGyver's co-worker is kidnapped by the boy's father and taken to Canada. MacGyver must go and retrieve the boy from the house of the boy's uncle, a powerful mob boss.

A man has been killed in broad daylight and Pete is at the scene. A stranger passes Pete by and whispers into his ear: "It's off." When Pete is looking at sketches of the suspects, MacGyver notices that Pete has trouble with his vision. Agent Stams from DXS arrives to meet Pete. Phoenix took on the job of returning Samantha Lora, a political fugitive, to her home country. Samantha's supporters were going to deliver a videotape stolen from San Pablo presidential palace showing summary executions of 200 political prisoners, when they ran into a death squad waiting for them. Pete was supposed to get the tape because they have a 6 p.m. deadline for a media conference about its contents at a local broadcasting station, but the man who has it took off when the death squad appeared and his whereabouts are unknown. Samantha is the only one who knows how to contact him. And for her, Phoenix has arranged a safe place until her transport to San Pablo leaves. Pete and MacGyver go to pick up Samantha when she arrives undercover. Samantha calls the number at which the man with the tape can be contacted. He then calls her back and agrees a time and place where he will deliver the tape. MacGyver gets to be the pick-up man. But underlings of the president of San Pablo are on his tail...

After his sister dies in an avalanche, Murdoc decides to resume working for his former employer, HIT. In order to regain their trust, he has to take on MacGyver once again.