W tajnej, podziemnej placówce badawczej w Bannon w stanie Nowy Meksyk dochodzi do wybuchu. Na skutek eksplozji z zabezpieczonych zbiorników zaczynają wyciekać toksyczne substancje. By nie dopuścić do zatrucia okolicznych wód, władze decydują się zalać placówkę wodorotlenkiem sodu. Na miejsce zostaje ściągnięty MacGyver, by uratować uwięzionych w środku naukowców. Rozpoczyna się walka z czasem.

W Birmie MacGyver ma przechwycić kanister ze śmiertelnie niebezpieczną substancją chemiczną. Trafia na obszar Złotego trójkąta, gdzie projekt rządowy przewiduje niewolniczą pracę miejscowych farmerów na plantacjach opium. Członkowie lokalnego kartelu narkotykowego podejrzewają, że MacGyver jest agentem wywiadu.

MacGyver travels to Budapest to meet with a Russian double agent who is in possession of a watch containing information about other Russian spies. However, before MacGyver can take the watch, the agent is killed and the watch is stolen. Now MacGyver must work with the Gypsies to get it back.

MacGyver attempts to get a reporter out of a Central American country with evidence linking a general to an illegal arms dealer. As they reach the border, it is clear escaping to Mexico will be no easy task, as the general and the arms dealer have every imaginable route severely guarded.

MacGyver comes along on a expedition to Brazil with his friend, entomologist Dr. Alden. They meet with a landowner and recluse, Trumbo, who is initially hostile. However, when they realize that a mile-wide column of army ants is moving through the jungle, they team together to mount a defense.

When MacGyver is on his way to a vacation, he takes the wrong way and ends up at a small airstrip where everybody seems to be behaving strangely. Too late, he discovers that the airstrip has been taken hostage, and he has been caught in the middle of a plane-hijacking attempt.

During a trip to visit some friends, an accident starts a fire in an oil well owned by MacGyver's friends. MacGyver and his buddy then go to fetch dynamite in an abandonned mine at great peril to themselves after they decide the dynamite is the only feasible way the fire can be put out. However, when they use it, the fire only becomes more intense. Can MacGyver and his Hellfire friend survive the incredible heat to put out the fire and save the oil buried underneath the well?

A man wants to testify against his mobster brother in Federal Court, and MacGyver has the job of keeping him safe, but the man's mother is dying and he wants to visit her.

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.