前軍情六處特工羅斯·泰勒招募鳳凰基金會前成員麥克、萊利、博茲、馬蒂和德西去追捕一種生物武器，該生物武器計畫被一個神祕組織用於對美國一個主要城市的毀滅性襲擊。

美国国防部将军约翰阿科斯塔（John Acosta）招募麦吉弗（MacGyver）从一个军事实验室窃取一个高度机密的项目，以发现其安全漏洞。但当发现将军计划使用武器发动攻击时，菲尼克斯必须在武器上传前阻止阿科斯塔。

当飞行员心脏病发作时，麦基弗和他的团队登上了一架正在飞行途中的飞机，发现这起医疗事故是故意的。

当麦基弗迅速从德国一座倒塌的建筑中营救幸存者时，他发现了一个新的安全威胁——一枚隐藏在废墟下的二战遗留下来的1000磅重的未爆炸物。

为了在法典中找到主要球员，并切断他们的假球资金，德西卧底潜入一支足球队，并找到与影子组织合作的腐败球员。

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 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.