Clay returned to the Pentagon in June 1952 as an Air Force member of the Joint Strategic Plans Group in the Organization of the Joint Chiefs of Staff. He later was assigned as chief of the Joint Plans Division, Deputy Chief of Staff, Operations, Headquarters U.S. Air Force. He went to Ramey Air Force Base, Puerto Rico, in July 1956 where he served as deputy commander of the 72d Bombardment Wing. In May 1958 he was assigned to Headquarters, Strategic Air Command (SAC) at Offutt Air Force Base, Nebraska, as chief of the Plans Division.