A Russian defector is helped by MacGyver to seek asylum in the U.S. Meanwhile, after Penny Parker comes to stay at MacGyver's for a few days, she accidentally uncovers an assassination plot of a foreign official.
A pregnant woman is on the run from her husband who wants her dead after she discovers his dark secret. MacGyver becomes trapped with the woman in an abandoned factory with her delivery inching nearer.
While MacGyver is at the viewing of this friend, Jack Dalton, two CIA agents gone bad show up to make sure Jack is dead. MacGyver is surprised to find out that Jack really isn't dead and that he is wanted for murder.
A pilot is on trial for being a spy in a Central American country and MacGyver is sent to rescue him. Matters become complicated when MacGyver discovers the pilot's daughter has stowed away on the rescue mission.