The events surrounding Boggs' death have been the subject of much speculation, suspicion, and numerous conspiracy theories. These theories often center on his membership on the Warren Commission. Boggs dissented from the Warren Commission's majority who supported the single bullet theory. Regarding the single bullet theory, Boggs commented, "I had strong doubts about it." In the Robert Ludlum novel, The Matarese Circle, Boggs was killed to stop his investigation of the Kennedy assassination.
Some tie Boggs' death to alleged corruption charges, or to his outspoken opposition to powerful Federal Bureau of Investigation director J. Edgar Hoover. Some people, including several of Begich's children, have suggested that Richard Nixon had a hand in Boggs' death in order to thwart the Watergate investigation. However, none of these theories has ever been proved, and one of Boggs' children -- journalist Cokie Roberts -- has publicly stated that the rumors about Boggs' wanting to reopen the Kennedy assassination case are completely false.