He left the music industry in the early 1990s and became a computer programmer. He later played bass in his son's band The Indestructible Beat of Palo Alto (IBOPA).
Stewart died on November 13, 2002, reportedly a result of "a long illness." However, Jamie Stewart has acknowledged that his father's death was, in fact, a suicide.
The track "Mike" from Xiu Xiu's album Fabulous Muscles concerns Jamie's reaction to his father's death.
Wounds to Bind: A Memoir of the Folk-Rock Revolution, a reminiscence by We Five co-founder Jerry Burgan incorporating Burgan's childhood friendship with Stewart, ponders Stewart's death, life and creative drive.