MacGyver’s mother Ellen MacGyver (Scottie Thompson) died when MacGyver was 5. James didn’t deal well with his wife’s death; becoming engrossed in his work at DXS. He eventually left with no warning when MacGyver was 10, leaving him in the care of Harry.
It was Harry who taught MacGyver to survive in the wild and to rely on his instincts. He also gave him his first Swiss Army Knife. According to a mention in Episode 2×12 (Mac + Jack), MacGyver and his roommate Wilt Bozer (Justin Hires) live in Harry’s house and the mortgage is paid off.
In the Season 2 Finale, it’s revealed that James MacGyver is Oversight and therefore not only the head of the Phoenix Foundation, but has also been MacGyver’s boss since he joined DXS. While he didn’t want to be found, he still kept tabs on MacGyver, staying in contact with Harry sporadically. Feeling betrayed, MacGyver hands in his resignation; stating that he can’t work for someone he doesn’t trust.
At the end of Episode 4×08 (Father + Son + Father + Matriarch), James sacrifices himself so MacGyver can escape and stop Codex from killing billions of people.
2×04 X-Ray + Penny