MacGyver is forced out of his grief over the tragic death of a friend by a madman with a score to settle from their past association.

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.

Mac and Jack return from a flight to find an abandoned baby in Jack's hangar, complete with a desperate note from the mother and his own endowment fund hidden in his diapers.

Central American rebels capture Pete and a nun during a coup d'état, and it's up to MacGyver and Jack to rescue them.

After Jack receives momentos of his father from an anonymous sender, he and MacGyver launch a search for Jack's mother, who's been missing since he was boy—and they aren't the only ones hunting for her.