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John Flynn was commissioned a Second Lieutenant in the Army Air Forces and awarded his pilot wings on May 23, 1944. After serving with a P-40 Warhawk Replacement Training Unit, Flynn was assigned to the 31st Fighter Wing in Italy, where he flew P-51 Mustangs on bomber escort missions until the end of the war. When the war ended, Flynn was transferred to the 20th Fighter Wing at Biggs AFB, Texas, where he flew P-51 Mustangs in aerial demonstration teams. He then attended the second Jet class at Williams AFB, Arizona, where he trained to fly the P-80 Shooting Star. His next assignment was as an RF-80 Shooting Star reconnaissance pilot with the 67th Tactical Reconnaissance Wing at March AFB, California. In August 1948, Flynn was transferred to the 49th Fighter Wing at Misawa AB, Japan. During this time, Flynn flew combat missions in Korea from June 1950 to February 1951. His next assignment was with the 20th Fighter Bomber Wing at Shaw AFB, South Carolina, and then at Langley AFB, Virginia, and finally at RAF Wethersfield, England. Flynn served as Chief of Plans for 19th Air Force at Foster AFB, Texas. He deployed with 19th AF to Adana, Turkey, for the Lebanese Contingency in 1958. He served at Headquarters USAF in the Pentagon from July 1959 to February 1963. Flynn next served as the Deputy Commander for Operations with the 49th Tactical Fighter Wing at Spangdahlem AB, West Germany, from August 1964 to June 1966, when he was made the Director of the Operational Readiness Inspection at Headquarters USAFE in Wiesbaden, West Germany. Colonel Flynn became Vice Commander of the 388th Tactical Fighter Wing, and began flying combat missions out of Korat Royal Thai AFB, Thailand, in August 1967. He was forced to eject over North Vietnam and was taken as a Prisoner of War after his F-105 Thunderchief was hit by a surface to air missile on October 27, 1967.

Colonel Flynn was released during Operation Homecoming on March 14, 1973. He was briefly hospitalized to recover from his injuries at Keesler AFB, Mississippi, and then became Vice Commandant of the Air War College at Maxwell AFB, Alabama, where he served from July 1973 to February 1974. General Flynn became Commandant of Air Command and Staff College, also at Maxwell AFB, in February 1974, and Commander of the Air Force Military Training Center at Lackland AFB, Texas, where he served from August 1974 to September 1976. His final assignment was as Inspector General of the U.S. Air Force from September 1976 until his retirement from the Air Force on October 1, 1978. General Flynn was a Command Pilot with over 4,500 flying hours in his Air Force Career. He was married to the former Mary Margaret Sullivan of Cleveland, Ohio, until his death on March 5, 1997, and they have five children-Sheila, Michaela, Bridget, Sean, and Kevin. Mary Margaret passed away on August 26, 1999, and was buried with her husband at the Fort Sam Houston National Cemetery in San Antonio, Texas.
- Air Force Cross
- Air Force Distinguished Service Medal (3)
- Silver Star
- Legion of Merit (3)
- Distinguished Flying Cross (7)
- Bronze Star
- Prisoner of War Medal