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

A general gives Phoenix a chance to regain its security clearance by testing a military lab's security, stealing a chip there. Things don't go as planned.

MacGyver and the team board a plane that's mid-flight when the pilot has a heart attack, and discover the medical emergency was intentional.

As MacGyver works quickly to rescue survivors from a collapsed building in Germany, he discovers a new safety threat - an undetonated bomb from World War II hidden beneath the rubble.

In an attempt to find the main players in the Codex and cut off their match-fixing funding, Desi goes undercover to infiltrate a soccer team and find the corrupt player working with the shadow organization.

When Russ's former love, Emilia, is kidnapped by the same rebels he fought during the military contract days, he takes the Phoenix team to a small, impoverished town to rescue her and rid the town of the rebels for good.

A double date descends into chaos when Mac and Desi witness a murder in the back of the restaurant, and as they work to find the killer, Riley tries to keep the secret about about their "day jobs" from her boyfriend, Aubrey

After Oversight is almost killed a bombing, he recruits Mac to help him find the suspected bomber; Mac meets his Aunt Gwendolyn.

Los Angeles' power grid is taken hostage in a ransomware attack resulting in a citywide blackout; the team discovers that the ransomware code used was written by Riley years ago.

Mac is placed inside a fake prison cell with a top Codex operative, The Merchant, in order to gain his trust and get intel on their next move.

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.

Mac and Riley continue their infiltration of Codex, and Gwen is torn in her loyalties. Russ and Desi both suspect Mac.