 Following his War College tour, Shelton served as the Deputy Program Manager and Executive Assistant for the Cooperative Threat Reduction Program Office which fell under the Office of the Assistant to the Secretary of Defense for Nuclear, Chemical, and Biological Defense Programs in Washington, DC.In 1996, he attended the Program for Senior Officials in National Security at Syracuse University and Johns Hopkins University.In September 1997 he assumed command of the 90th Space Wing at Francis E. Warren AFB in Wyoming.