In Vietnam, he logged the most hours of any pilot on F-8 Crusader supersonic jets. After the war he flew photo reconnaissance missions. In 1987, he became a rear admiral, posted at the Pentagon for the Naval Reserve. He helped organize the 1991 Tailhook conference, and became embroiled in the ensuing sexual harassmanet scandal. On October 15, 1993 he was censured, effectively ending further advancement. He retired from the Navy in 1995, became a pilot for American Airlines, and retired from that occupation. He remained available for technical advice to the Pentagon, where he had an office.
Flagg moved to Millwood, Virginia around 1993 to start Daybreak Farm, a cattle farm.
Flagg died at 62 in the crash of American Airlines flight 77 in the September 11, 2001 Terrorist Attack. He was traveling with his wife, Darlene "Dee" Flagg, and friend, Barbara G. Edwards, to Las Vegas at the time of the crash.
He is survived by two sons, including Michael Flagg, and other family.