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Secord served as a flight instructor from 1956 to 1959 at Laredo Air Force Base, and from 1959 to 1961 as an instructor and operations officer at Tinker Air Force Base. During the latter assignment, he was posted to the University of Oklahoma to study for a master’s degree in English Literature. While progressing to the point of needing only his thesis to gain his degree, he met and married his wife, Jo Ann.
In August 1961 he joined covert operations in what would become the 1st Air Commando Wing, remaining there until 1965. As part of Operation Farm Gate, the wing was the first American aviation unit assigned to Vietnam. Secord flew over 200 combat missions between March 1962 to January 1963, flying AT-28s. One of the Vietnamese pilots he met during this assignment was Nguyen Cao Ky, later the president of Vietnam. Another new acquaintance there was Brigadier General Harry “Heinie” Aderholt. Also during this time, Secord was temporarily assigned to the Imperial Iranian Air Force as an adviser (January to July 1963, January to May 1964, January to March 1965).
After graduating from the Air Command and Staff College in 1966, Secord returned to Vietnam as an air operations officer, before being transferred to Thailand’s Udorn Royal Thai Air Force Base in August 1966. Belatedly promoted to major, he joined Operation Waterpump to train the Royal Lao Air Force. During this time Secord was detailed to the Central Intelligence Agency to serve in the Secret War in Laos. He worked for, and knew, Ted Shackley and Thomas Clines; he worked directly with the CIA officers supplying the Secret War in Laos, James William Lair and Lloyd C. “Pat” Landry.
On 7 January 1967, in what is still a heavily classified operation, Secord directed the only successful prisoner of war rescue of the Vietnam War, the Ban Naden raid. A team of the CIA’s hill-tribe mercenaries was inserted out of hearing of the POW prison; their surprise raid quickly wiped out about 40 guards. It was then discovered there were about twice as many prisoners as expected. Nevertheless, a scratch force of nine single-piloted Air America H-34 helicopters dropped into the middle of the Hồ Chí Minh Trail and rescued 53 Asian prisoners. This rescue is still used as a case study in CIA training for covert operations.
Secord’s responsibilities as a one-man logistics and operations staff covered a wide range of duties. One of the first duties he assumed was defense of Lima Site 85. In early 1967, General Hunter Harris briefed Secord and Lair on the upgrading of the TACAN installation there with guidance radar. The location, nearly on the Lao border with northern Vietnam, would enable American strike aircraft to follow its radar beam to Hanoi or Vinh and drop their bombs blind, regardless of weather. Lair and Secord were tasked with defense of the site. Despite their best efforts, this site would be overrun in March 1968. Secord requested additional protection for the sheep-dipped technicians. Ambassador William H. Sullivan, who supervised the war in Laos by presidential directive, denied the need for stationing Green Berets at the site, or for personal weaponry. However, Secord insubordinately issued small arms to the onsite technicians for self-defense.
Having flown 285 combat missions in Southeast Asia, Secord mulled resigning from the USAF. General Aderholdt convinced him to reconsider. During Secord’s next posting, he was promoted to lieutenant colonel ahead of his peers. Secord served at Eglin Air Force Base from September 1968 to November 1969, as assistant deputy chief of staff for operations for the Tactical Air Command, in what would later become the U.S. Air Force Special Operations Force. From there, he transferred to serve as commanding officer of the 603rd Special Operations Squadron. His three years in command of the 603rd was focused on development of the A-37 Dragonfly for counter-insurgency; however, the 603rd was disbanded in June 1971. Secord moved on, to attend the Naval War College in August 1971.