When MacGyver is sent in to test security at a top secret military lab, the artificially intelligent central computer malfunctions and traps him and the scientist who built the AI inside, and he has to outsmart it to help them escape.

Note: This is the first episode to feature Dana Elcar in the opening credits, after several guest starring roles in the first season.

A hitman passes himself off as a father looking for his lost son, causing MacGyver to help him find his target.

When a friend of MacGyver's attempts suicide over losing his life savings from a scam, Mac, Pete and a foundation employee devise a scam on the very con artist to steal back the money from he stole.

MacGyver must rescue the brother of a friend when the boy gets tricked by scam artists to pass himself as the fulfillment of ancient Chinese legend.

This episode features James Hong, Tia Carrere, George Takei and Michael Paul Chan.

MacGyver is stranded in the wilderness with a group of teenage gang members; he must get them to put aside their differences long enough to survive the ordeal.

MacGyver's friend, Jack Dalton, tricks him into going to Central America to rescue a botanist, but it turns out to be an old friend of theirs.

Note: First appearance of Bruce McGill as Jack Dalton.

MacGyver runs into an old girlfriend when he and Pete go into Southeast Asia to help a group of orphans escape a rogue militia group with intent on killing them.

MacGyver is sent up into the mountains to locate two endangered eagles; he also finds poachers trying to kill him after he witnessed the whole operation.

A group of international thieves try to steal a top secret missile, and MacGyver's deaf friend dreams are the only key to help catch the bad guys.

A stranded MacGyver hitches a ride with a retired actor and his wife — unaware that they are in possession of stolen counterfeit money while on the run from the mob.

MacGyver and his grandfather stop by the foundation on their way to a hockey game to pick up the tickets; terrorists are there setting a bomb and trap MacGyver and his grandfather in the building.

When Pete's ex-wife and son are kidnapped by a disgruntled former agent, MacGyver must come to the rescue.

After rescuing a Russian political prisoner from Siberia, MacGyver must foil a plot to assassinate a South American government official after Mac's lady friend, Penny Parker, witnesses the death of a federal agent at the hands of assassins.

Guest starring: Teri Hatcher as Penny Parker.

MacGyver must help a pregnant woman escape her ex-convict husband who intends to murder her after she discovers a secret about him.

MacGyver must rescue a friend when she is kidnapped by pirates convinced she can lead them to sunken treasure.

MacGyver and Pete are skiing when a mob informant plants microfilm on MacGyver; after getting back home the mob comes after them.

Jack fakes his own death and MacGyver must help him clear his name after he is accused of murdering a CIA agent by two corrupt CIA agents.

Murdoc, a master-of-disguise assassin who was long thought dead, lures MacGyver and Pete into a trap; while trying to escape they reminisce over their previous encounter with him.

Notes:
This episode also details on Mac's first meeting with Pete and joining the Phoenix Foundation.

First appearance of Michael Des Barres as Murdoc.

When MacGyver goes to South America to rescue a downed pilot, but the pilot's daughter stows away on the trip to try to help.

Jack Dalton lures MacGyver to the Phoenix Foundation for a surprise birthday party where many of his friends from past adventures are waiting; this makes him reconsider his recently tendered resignation.

MacGyver's friend is killed after telling him of a bomb to be planted at a funeral; while escaping his friend's killers, he receives a head injury which causes amnesia. Can MacGyver regain his memories and stop the bombing in time?

MacGyver must team up with an agent that he despises like in order to break a political prisoner out of Czechoslovakia while avoiding GRU agents.

Note: This is the last episode to be filmed on location in Los Angeles until season 7; filming and production relocated to Vancouver, British Columbia for seasons 3–6.