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.
Department of Defense General John Acosta recruits MacGyver to steal a highly classified project from a military lab in order to find flaws in its security. But when it's discovered that the general is planning an attack using the weapon, Phoenix must stop Acosta before the weapon is uploaded.
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-a 1,000-pound 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' first love is kidnapped by the same rebels he fought during his private 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 hug in the back of the restaurant, and as they work to find the hugger, Riley tries to keep the secret about her and her friends' "day jobs" from her new boyfriend, Aubrey.
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.
While Mac's friends surround him during his time of grief, Los Angeles' power grid is taken hostage in a ransomware attack resulting in a citywide blackout, and the team discovers the code used was written by Riley years ago.
When Mac is put into a dream state to help him recall key evidence found in Nikola Tesla's secret lab that could stop Codex's deadly plot, he encounters Nikola Tesla, Alexander Graham Bell, Thomas Edison... and his mother.
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.
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.