His wife Ellen (Scottie Thompson) died when MacGyver was 5. James didn’t deal well with her death; becoming emotionally distant to his son due to constantly feeling angry. He eventually left when MacGyver was 10, leaving him in the care of Harry.
Season Zero (offscreen)
The Phoenix Foundation and its predecessors have a history of teaming up soldiers with scientists. For 13 years, Jonah Walsh (Brad William Henke) was James’ partner in field missions for DXS and his closest friend – until he switched sides. Even after James was appointed Oversight of the Phoenix Foundation, he never stopped looking for Walsh.
After Director of Field Operations Patricia Thornton (Sandrine Holt) was arrested for being a mole, James authorized CIA operative Matty Webber (Meredith Eaton) to investigate him as part of her interview as a possible replacement to Thornton.
In the beginning of Season 1, Jack Dalton (George Eads) urges MacGyver to get in contact with James; knowing from his own experience that Mac might regret wasting so much time to make up with his father. MacGyver agrees to write him a letter.
In the Season 1 Finale, MacGyver tells Jack that the letter got returned and he can’t seem to find another way to contact James. Jack agrees to accompany Mac to go looking for him.
In the Season 2 Premiere, Mac and Jack are called back to work after being more or less unsuccessful in finding James.
During the season, MacGyver follows several clues that James seemingly left him. Frustratingly, the clues seem to lead to nowhere. Later in the season, Jack enlists Elwood Davis (Billy Baldwin) and Matty’s personal assistant Jill Morgan (Kate Bond) to help him break into Matty‘s house and steal documents from her safe; confirming the suspicions that Matty knows James and even investigated him years ago. When Mac confronts Matty about it, she denies having ever met James MacGyver.
In the Season 2 Finale, MacGyver meets up with Matty to quit since he still feels she’s hiding the truth. It’s later revealed to the audience and Team Phoenix that James MacGyver is Oversight and therefore not only the head of the Phoenix Foundation, but also actually MacGyver’s boss since he joined DXS. It was also him that arranged for MacGyver and Jack being partnered up in Afghanistan. Feeling betrayed, Mac hands in his resignation; stating that he can’t work for someone he doesn’t trust.
In the Season 3 Premiere, James MacGyver visits his son in Nigeria; stating that he needs to come back because Jack got himself in trouble. As it turns out, Jack had tried to find James’ nemesis Jonah Walsh on his own so James had a reason to resign and Mac could come back to Phoenix. Although MacGyver agreed to come back for just this one mission, he then decides to stay with Phoenix to catch Murdoc (David Dastmalchian).
After becoming suspicious that James is once again hiding things from him in Episode 3×17, MacGyver discovers that James has Stage 4 cancer and is receiving regular chemotherapy.
In the Season 3 finale (Mason + Cable + Choices), Charlie Robinson (Emerson Brooks) is used as a pawn against Mac and James; locked in an elaborate trap that either kills him or sets off a bomb underneath a fully-booked hotel. Charlie asks Mac to find his murderer, then sacrifices himself to save his friends and the hotel-guests. Although they catch Elliot Mason (Peter Weller) within the same episode, he manages to escape.
At the end of the episode, James confesses to MacGyver that he sacrificed Masons son during a mission to get his own son rescued. Mac is appalled that his father favored his life over that of another agent – especially without that agent and his team knowing about the risks.
After the events in the Season 3 Finale, the Phoenix Foundation was disbanded and the team members were stripped of their high-level clearances. In Episode 4×01 (Fire + Ashes + Legacy = Phoenix), Russ Taylor (Henry Ian Cusick) as the new owner of Phoenix approaches MacGyver; convincing him to get “Team Phoenix” back together.
While MacGyver didn’t have any contact with James for months, Matty contacts Oversight in Episode 4×07 (Mac + Desi + Riley + Aubrey). She visits him in the hospital, talking to him about her suspicions of James’ sister-in-law Gwendolyn Hayes (Jeri Ryan) still being alive and involved with Codex.
When trying to track down Mason in Episode 4×08 (Father + Son + Father + Matriarch), James reveals to MacGyver that his cancer is back and that he probably has only a few months left. They find Mason, but soon realize that it was all a trap and that Gwendolyn is indeed still alive. She tells MacGyver that File 47 was actually his mothers idea; trying to convince her nephew to join Codex and “reset the world” together.
At the end of the episode, James sacrifices himself so MacGyver can escape; pointing out beforehand that his son is the more valuable asset and the only one who can stop Codex from destroying the world.
Reboot series (recurring character)2×23 MacGyver + MacGyver
3×04 Guts + Fuel + Hope
3×05 Dia de Muertos + Sicarios + Family
3×17 Seeds + Permafrost + Feather
3×18 Murdoc + Helman + Hit
3×20 No-Go + High-Voltage + Rescue
3×21 Treason + Heartbreak + Gum
3×22 Mason + Cable + Choices
4×07 Mac + Desi + Riley + Aubrey
4×08 Father + Son + Father + Matriarch
4×09 Code + Artemis + Nuclear + N3mesis