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.
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
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.
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.
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.
Matty splits the team up for a mission, and partners the teammates with their fellow teammates they had the most problems with during the Codex affair.
When Taylor's former protégé is killed while preventing a bio-weapon from falling into the wrong hands, Mac and the team must find the weapon so Desi can pull off the ultimate heist before it's sold to a terrorist cell.
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.