Matty reveals a shocking secret to the team: she has a husband who’s been undercover in a criminal organization called S-Company for eight years. When his status as a CIA agent comes out, Matty needs MacGyver to find and extract her husband before it’s too late.

Ex-MI6 agent Russ Taylor recruits former Phoenix Foundation members Mac, Riley, Bozer, Matty and Desi to hunt down a bioweapon that’s planned to be used by a mysterious organization for a devastating attack on a major U.S. city.

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.

When Russ is kidnapped, Mac and the team must break out a previously murderous psychopath, now pacifist, from prison to help find him. Also, while on the run, Mac and Desi are forced to confront their relationship issues.

The secret experimental cancer treatment Mac’s developing with a friend is discovered when culprits ransack their lab, kidnap Mac’s partner and plan to use the research to create a powerful new nerve agent.