The Phoenix Foundation and its predecessors have a history of teaming up soldiers with scientists. For 13 years, Jonah Walsh (Brad William Henke) was the partner of James MacGyver (Tate Donovan) in field missions for DXS. He was also James’ closest friend until he switched sides.
As an ex-DXS agent, Jonah Walsh is a highly trained former U.S. operative. Walsh is the number six on Interpol’s Most Wanted list. With his terrorist partners, he’s been living in the shadows for years, using encoded communications.
In the Season 2 Finale Episode 2×23 (MacGyver + MacGyver), Angus MacGyver (Lucas Till) meets up with his boss Matty Webber (Meredith Eaton) to quit since he still feels she’s hiding the truth about his father. It’s later revealed to the audience and Team Phoenix that James MacGyver is actually Oversight and therefore not only the head of the Phoenix Foundation, but also MacGyver’s boss since he joined DXS.
Since MacGyver interrupted his dad on a mission to track down Jonah Walsh, Mac and Jack Dalton (George Eads) join in to help. In Mexico, they find Walsh’s hideout place and realize that Walsh and his cartel friends are trying to re-create a drug that turns humans into ultimate soldiers. Walsh threatens to shoot MacGyver; forcing James to finish the drug for him. Mac and James pretend to finish the drug just before destroying the lab by setting it on fire. With the help of Jack, they manage to get out just in time, but Walsh is able to escape.
Back home, MacGyver hands in his resignation; stating that he can’t work for someone he doesn’t trust.
In the Season 3 Premiere, James tells MacGyver that Jack got himself in trouble and needs help. As it turns out, Jack had tried to find Walsh on his own so James had a reason to resign and Mac could come back to Phoenix.
Reboot Season 2
2×23 MacGyver + MacGyver
Brad William Henke