After blowing away a nuclear facility under the control of an aggressive world leader, MacGyver returns home for some peace and quiet, only to find his boss waiting for him. He advises MacGyver that a contract is out on his life and he needs to skip town for awhile.

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.

MacGyver is trapped in a mansion with Pete, a code expert, and a government agent who may or may not be on their side. However, an old nemesis has electronically booby-trapped the entire mansion to make sure they can't go anywhere.

An old girlfriend of MacGyver's contacts him for help after she discovers evidence of uranium thefts from a nuclear processing plant where she works.

A mysterious person who calls himself "Viking" has just bombed the cruise ship Victoria, underway in the North Pacific Ocean. He demands six million dollars or another bomb will go off within hours. So MacGyver gets called in, along with his old Vietnam bomb-defusal partner, Charlie Robinson, to disarm it. But when they get there, they find out there's more than one bomb on the ship. Complications arise when MacGyver's partner sets off one of the bombs, and the bomber decides that DXS operated in bad faith and refuses to hand over the bomb-disarming instructions after he gets the extortion money.

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.

MacGyver is on his way out of Bulgaria with a secret microfilm, when he meets Penny Parker, a beautiful, talkative American, who is on the run from her lover, a man named Stephan Frolov. She stashes some jewels on MacGyver, thus making him a suspect, and now MacGyver and Penny must flee Bulgaria together.

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.

A 15-year-old genius accidentally hacks into a defective missile guidance system and attracts the attention of both the FBI and some black marketeers, who think that she may fix it for them. It's up to MacGyver to save her from being kidnapped by either side.

At the beginning of the episode, MacGyver literally has to jump onto a moving train that he missed earlier to return top-secret files and documents to the U.S. Government. Soon after, a local tribe stops the train. They take all passengers hostage until the men responsible for the death of the tribal leader's son is found among the passengers.

When a mother superior at a religious mission in North Africa asks MacGyver to help a young woman with something, he is glad to help. However, when he finds out the young woman wants him to break her brother out of jail, he may have taken on more than he expected.

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.

Posing as a watchmaker who manufactures bomb timers, MacGyver manages to catch a master killer—Piedra—before he attempts an assassination on a high-profile target. However, Piedra isn't about to be stopped for long.