MacGyver accompanies Penny Parker to an old house she inherited from her Aunt Betty, who mysteriously died 30 years before. When strange things start happening, Penny is sure that the house is haunted.

MacGyver returns to his home town of Mission City, Minnesota to meet up with two old friends, Chuck and Neil, so they can dig up a time capsule they buried twenty-five years before. However, MacGyver is hesitant to dig the capsule up because he is still haunted by the death of his old friend Jesse, who died when MacGyver was young. But now MacGyver has another problem to deal with. Chuck's and Neil's sons, Danny and Sean, have gotten wrapped up in a drug deal, and the dealer is after Danny. Danny takes off to hide, and now MacGyver must find him, before the drug dealer does.

MacGyver helps an Amish family, who saved his life, from having their farm seized by the government.

Central American rebels capture Pete and a nun during a coup d'état, and it's up to MacGyver and Jack to rescue them.

When a friend of Mac's is injured in a crash, Mac agrees to test the new racing engine designed by the Phoenix Foundation. However a business rival has other plans for him, and he has someone from the inside to help him.

While on assignment to test field agents for the Phoenix Foundation, MacGyver and Pete discover the wreckage of a DEA plane shot down by dangerous drug smugglers.

MacGyver gets involved in the search for an escaped serial killer. Soon he comes to the conclusion that the killer had help from another prisoner—an even more sinister man.

After Jack receives momentos of his father from an anonymous sender, he and MacGyver launch a search for Jack's mother, who's been missing since he was boy—and they aren't the only ones hunting for her.

Penny Parker's big chance in a major professional role is threatened from two directions: a money shortage and several deaths linked to the musical she is set to perform in.

Pete is conflicted when he discovers that the Phoenix Foundation employee selling classified information turns out to be his son.

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

An inner city youth club is threatened when a black resident is framed for auto theft by a neighborhood racist who'll stop at nothing to close the center—even murder.

MacGyver helps a young runaway with a vicious pimp and a tragic secret about her policeman father.

MacGyver joins a joint U.S.-U.S.S.R. team trekking into the Alaskan wilderness to retrieve a huge amount of Russian gold from a downed plane only to learn that someone has beaten them to it.

MacGyver heads up a trip with four other Phoenix Foundation employees into the wilderness as part of a stress reduction program. After discovering that a prison bus accident has freed several prisoners, the employees begin to question each other's behavior. MacGyver must now figure out which man, if any, is not to be trusted before it's too late.

Jack Dalton is brainwashed by an African politician and his wife to assassinate the leader of an African nation, who is in town for an awards ceremony.

MacGyver works hard to retrieve the anthrax bacillus stolen by a former Navy commando who once saved his life, and is now suffering the effects of an old head wound.

Jack, MacGyver, and Pete review their past adventures while on a gold-panning expedition, unaware they're being stalked by a vengeful killer.