In 1984, Johnson reported to the U.S. Air Force Test Pilot School at Edwards Air Force Base, California. After graduation, he reported to Naval Weapons Center China Lake, California, performing flight tests in the A-6E Intruder and F/A-18A Hornet aircraft. Following his flight test tour, then Lieutenant Commander Johnson returned to NAS Whidbey Island for his department head tour in an operational A-6 squadron. Following refresher training and an instructor tour at VA-128, he reported to Attack Squadron 196 (VA-196), serving as both an A-6 pilot/mission commander and the squadron's Aircraft Maintenance Department Head. During this tour he completed another Western Pacific and Indian Ocean deployment as well as a Northern Pacific deployment.