After Oversight is almost killed in a bombing, he recruits Mac to help him find the suspected bomber, Mason. However, when Mason reveals he didn’t plant the bomb, the three team up to track down Codex, the shadow organization that set them up. Also, Mac meets his aunt Gwendolyn.

The Phoenix team is forever altered when MacGyver’s Aunt Gwen gets into his head about family and connection and convinces Mac and Riley to join Codex. Also, Matty and Russ take their concerns about Codex to the White House.

With Mac and Riley undercover with Codex, hoping to stop the organization from within, their mission is interrupted when Russ, Desi and the Phoenix team move to prevent Codex from detonating a weapon of mass destruction, with Mac and Riley caught in the crosshairs. Also, the team discovers Russ’ real reason for purchasing the Phoenix Foundation.