MacGyver follows the adventures of the laid-back, extremely resourceful secret agent Angus MacGyver. He prefers non-violent conflict resolution whenever possible and refuses to carry or use a gun. MacGyver works as a problem solver for the Phoenix Foundation in Los Angeles. Utilizing his education as a scientist and his experience as an operative in the Department of External Services (DXS), he is able to solve a range of problems usually with the help of his ever-present Swiss Army knife.
MacGyver accompanies his friend Penny Parker to an old house she has inherited from her Aunt Betty, who mysteriously died 30 years before. When strange things start happening, Penny is sure that the house is haunted. However, MacGyver tries to convince her that there's no such thing as ghosts, but then he starts witnessing the strange events, too.
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, and it's up to Mac and Jack to rescue them. But, Jack's plane is sub par, and they go down in the middle of enemy territory.
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 for the Phoenix Foundation to test field agents to make sure they are still in shape, MacGyver finds out he now has another agent to test: Pete. Things take a turn for the worse when MacGyver and Pete head into the wilderness where they stumble upon a wrecked plane and pictures of two dangerous drug smugglers who shot it down.
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.
Jack receives mementos of his father from an anonymous sender. This triggers a search for Jack´s mother, who has been missing since Jack was a boy. But when he finally gets to meet her, she turns out to be a fugitive in fear of her life, and Jack´s presence only complicate things more.
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.
When Pete's son, Michael, returns to work for the foundation, neither Pete nor MacGyver see that Michael has used his connections to get closer to a Phoenix Foundation technology system in order to steal it and to sell it to the mysterious Papillion. But Papillion has plans of his own for Michael and his gang.
When a kid is kidnapped by his estranged father, MacGyver tries to help the mother, a Phoenix employee, to rescue the boy. But the father is the son of an aging organized crime kingpin whose control is being threatened by subordinates.
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 and Pete are captured by terrorists intent on wiping out a nearby city with an electromagnetic pulse, unless their leader is freed.
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.