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.

When Pete's son, Michael, returns to work for the foundation, neither Pete nor MacGyver see that Michael has used his connections to get closer to a Phoenix Foundation technology system in order to steal it and to sell it to the mysterious Papillion. But Papillion has plans of his own for Michael and his gang.