While there, he participated in the Navy's preliminary evaluation and Board of Inspection and Survey trials of the F-14 Tomcat and tested a leading edge slat modification to the F-4 Phantom.

Among his technical assignments, he served as Astronaut Office Safety Officer; technical assistant to the Director of Flight Crew Operations in 1981; a chase pilot on STS-1; software verification at the Shuttle Avionics Integration Laboratory (SAIL); mission support group leader for STS-5 and STS-6; Assistant to the Director, Flight Crew Operations; leader of the astronaut support team at Kennedy Space Center in 1985; Branch Chief, Space Station Design and Development; and Special Manager for Assembly, Space Station Project Office.

From July 1993 to June 1994, Walker was Chief of the Station/Exploration Support Office, Flight Crew Operations Directorate, after which he chaired the JSC Safety Review Board.

Walker was in training to command STS-61-G, scheduled for a May 1986 launch when the Challenger disaster forced NASA to suspend all Shuttle flights.

In 1989, while piloting a NASA T-38 Talon to Washington, D.C. for ceremonies honoring the crew of STS-30, Walker came within 100 ft (30 m) of striking a Pan Am jetliner.

In addition, the crew also worked on secondary payloads involving fluid research in general, chemistry, and electrical storm studies.

STS-53 Discovery (December 2–9, 1992) was launched from the Kennedy Space Center, Florida, and also returned to land at Edwards Air Force Base, California.

During 115 Earth orbits, the five-man crew deployed a classified Department of Defense payload DOD-1 and then performed several Military-Man-in-Space and NASA experiments.

In April 1996, Walker retired from the Navy and left NASA to become Vice President for sales and marketing for NDC Voice Communications in San Diego, California.