When MacGyver comes home with some important documents, he's drugged by enemy agents and told that he will die in six hours if he doesn't retrieve the documents for them. But MacGyver, using an old prisoner trick, escapes. Now the only problem is convincing someone that he's not just another drunk.

After a daring escape from East Germany where he gets rescued, and in the process saves a fellow operative with a quick mechanical fix, MacGyver thinks that he deserves some peaceful vacation time. But Pete lures him into baby-sitting a Russian defector who can identify KGB agents.

In Afghanistan, wounded and hunted by the Soviets, MacGyver is given refuge by an Afghan woman and her son. But they are themselves at the mercy of an Afghan thug, who will kill MacGyver if he finds him at his woman.

Pete Thornton investigates the supposed death of an old friend, a prominent Russian dissident, and finds he must get his friend's daughter Maria out of the country before the secret police arrest her for an alleged conspiracy. However, while in Russia, Pete bumps into MacGyver, who followed him from the United States. While disappointed MacGyver followed him, Pete gladly welcomes MacGyver into his plans when the secret police arrive to take Maria into custody. Following a high speed boat chase to escape the police, Pete and MacGyver find out from Maria that her father is not dead, he is being held in a maximum security ward at a state mental institution. To get into the mental hospital, MacGyver plays the part of a mad patient and Pete plays the part of a doctor who has been assigned to him. With the help of the other patients, MacGyver is able to escape into Ward Zero, where Pete's friend is held. MacGyver breaks him out and hides him with the other patients.

MacGyver and Pete head to Asia to rescue a nun, who is an old friend of Pete's, and the orphaned children she takes care of from aggressive regime troops. While there, MacGyver runs into someone he never expected, his old fiancee, Debra. Now MacGyver must complete his mission, work out his differences with Debra, and escape from the troops, all before the troops find them.

When MacGyver and Pete go skiing, a man switches poles with MacGyver, only moments before being gunned down and killed by his former friends. But the gunshot starts an avalanche, which covers MacGyver completely, leaving it up to Pete to convince the mountain rangers to stage a search and rescue before the next avalanche comes. As MacGyver finally is dug up, the gangsters are there, waiting for him, and whatever is hidden in that ski pole.

MacGyver and Pete meet at a wrecking yard, both thinking that the other one arranged the meeting. Soon an unknown assailant captures them inside a big truck. Their only clue is an obituary for them and Jack Dalton.

MacGyver's friends throw a birthday party for him, but he's somberly reflecting on his past and future. While reflecting, MacGyver decides to leave the Phoenix Foundation to get married and have a family. Can Pete convince him of how important he is to the Foundation and get him to change his mind?

MacGyver is called to a meeting with a former British spy, who has learned of a group of terrorists that will use a new plastic explosive in a vengeful attack on the U.S. army. This explosive can be hidden anywhere. However, before the spy can give MacGyver all the details he is shot. MacGyver flees through a window and is picked up by a boat. The female who owns the boat soon learns that the man she has rescued doesn't have any memory.

While helping the People's Republic of China secure a priceless national treasure—The Ming Dragon—in a San Diego museum, MacGyver runs into a Lisa, a woman that he had loved and thought was long dead. MacGyver learns that Lisa has been alive all these years and needs his help escaping the KGB.

The KBG have Lisa in their grasp, and MacGyver must get The Ming Dragon for them to free Lisa. MacGyver enlists the help of his old buddy, Jack Dalton, to help him steal it.

MacGyver teams up with colleague Nikki Carpenter to find out who is behind the attempts on her life. When they find out that the man who tried to kill her is connected to two terrorists who blew up a local post office, MacGyver and Nikki must find out what the terrorist's next target is before it's too late.

While testing a new nuclear bomb defusing team at the Phoenix Foundation, a deadly explosion kills three men. Pete blames himself for not inspecting their equipment better and resigns from his job out of guilt. However, Pete is replaced by a not-so-trustworthy man—one who may have been connected to the explosion.

While back in Minnesota to fill in as coach for a high-school hockey team, MacGyver tries to change the attitude of a callous player who has a shot at playing for the pros. But when this kid's ambition lands another player in the hospital, MacGyver must try and find out what or who is pushing him so hard to succeed.

Jack and Mac help an ancient Indian search for a wolf mask that two mercenaries are also eager to have.