While on assignment for the Phoenix Foundation to test field agents to make sure they are still in shape, MacGyver finds out he now has another agent to test: Pete. Things take a turn for the worse when MacGyver and Pete head into the wilderness where they stumble upon a wrecked plane and pictures of two dangerous drug smugglers who shot it down.

Jack receives mementos of his father from an anonymous sender. This triggers a search for Jack´s mother, who has been missing since Jack was a boy. But when he finally gets to meet her, she turns out to be a fugitive in fear of her life, and Jack´s presence only complicate things more.