On July 23, 1959, Stewart was promoted to brigadier general. During his active duty periods, he remained current as a pilot of Convair B-36 Peacemaker, Boeing B-47 Stratojet and Boeing B-52 Stratofortress intercontinental bombers of the Strategic Air Command. On February 20, 1966, Brigadier General Stewart flew as a non-duty observer in a B-52 on an Arc Light bombing mission during the Vietnam War. He refused the release of any publicity regarding his participation, as he did not want it treated as a stunt.

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