Deep in the Amazon jungle, a horde of killer ants is destroying everything in its path. MacGyver helps his entomologist friend and the plantation owner to battle the ants before the plantation is destroyed.
MacGyver is assigned to protect a person in the Federal Witness Protection Program. The man he is protecting wants to come out of hiding to visit his dying mother. MacGyver must protect him from the Mob and from the Feds.
MacGyver is kidnapped by enemy agents to retrieve sensitive information he stole from them. To get him to talk, they inject MacGyver with a hallucinogenic drug that will kill him in six hours, unless an antidote they have is administered.
A cruise ship is the target of a terrorist attack and has three bombs hidden aboard. MacGyver and a friend from the agency are asked to dismantle the bombs before it's too late for the crew and passengers.
In Bulgaria, MacGyver collects a top-secret microfilm and attempts to smuggle it out of the country. At the airport he meets a mysterious beautiful American girl, who turns out to have ties to the Bulgarian Secret Police.
While on a rescue mission in Soviet Afghanistan, MacGyver is shot and wounded. An Afghan woman and her son risk their lives to give refuge to MacGyver. A wounded MacGyver must now outwit the Russian Army to complete his mission.