Johnson resigned his Regular Navy commission in 1990 and transferred back to the Naval Reserve while accepting a concurrent civil service position with the National Aeronautics and Space Administration (NASA) at the Johnson Space Center (JSC) Aircraft Operations Division at Ellington Field, Texas. In his concurrent military capacity from 1990–2007, he was promoted to Commander and later to Captain in the Navy Reserve and was the Commanding Officer of four Navy Reserve units. He also served as a Senior Research Officer in a Science and Technology Unit of the Office of Naval Research based at the U.S. Naval Postgraduate School in Monterey, California.