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Gene Pemberton enlisted in the U.S. Army Reserve on January 25, 1944, and went on active duty in the U.S. Army Air Forces on December 7, 1944. After completing basic training and flexible gunnery training, Corporal Pemberton served at Keesler Field, Mississippi, from November 1945 until his discharge from active duty on August 2, 1946. He remained in the Air Force Reserve until July 5, 1951, having been promoted to second lieutenant in the reserves on April 6, 1951. Lieutenant Pemberton went on active duty for pilot training on July 6, 1951, and was awarded his pilot wings at Vance AFB, Oklahoma, in July 1952. His next assignment was as an F-47 Thunderbolt pilot with the 136th and then the 47th Fighter-Interceptor Squadrons at Niagara Falls ARS, New York, from August 1952 to March 1954, followed by service as an F-86 Sabre pilot with the 334th Fighter-Interceptor Squadron at Chitose AB, Japan, from May 1954 to July 1956. Captain Pemberton completed F-100 Super Sabre Combat Crew Training and jet instructor training in November 1956, and then served as a fighter gunnery instructor with the 3594th Combat Crew Training Squadron at Nellis AFB, Nevada, from November 1956 to April 1958. His next assignment was as an Air Operations Officer with the 3595th and then the 4520th Combat Crew Training Wings at Nellis AFB from May 1958 to September 1961, followed by service as an F-105 Thunderchief pilot with the 23rd Tactical Fighter Squadron of the 36th Tactical Fighter Wing at Bitburg AB, West Germany, from September 1961 to September 1964. Major Pemberton next served as an F-105 pilot with the 561st Tactical Fighter Squadron and the 23rd Tactical Fighter Wing at McConnell AFB, Kansas, from September 1964 to July 1966, during which time he deployed to Southeast Asia from March to June 1965. He deployed to Southeast Asia with the 354th Tactical Fighter Squadron at Takhli Royal Thai AFB, Thailand, in early July 1966, and was forced to eject over North Vietnam and was taken as a Prisoner of War on July 23, 1966.

Major Pemberton was reported to have died in captivity the next day, on July 24, 1966, but he was officially listed as Missing in Action until the end of the war, having been promoted from Major to Colonel during this time. His remains were returned to the United States on March 6, 1974, and he was buried at the Graceland Memorial Cemetery in Cameron, Missouri.
- Silver Star
- Prisoner of War Medal