After completing jet training in the TA-4J Skyhawk, Scott served a tour of duty with Fighter Squadron 84 (VF-84) at NAS Oceana, Virginia, flying the F-14 Tomcat. In June 1986 he was designated an Aerospace Engineering Duty Officer (AEDO). He served as a production test pilot at the Naval Aviation Depot, NAS Jacksonville, Florida, flying the F/A-18 Hornet and the A-7 Corsair aircraft. He was also assigned as Director of the Product Support (engineering) Department. He was next assigned as the Deputy Director of the Tactical Aircraft Systems Department at the Naval Air Development Center at Warminster, Pennsylvania. As a research and development project pilot, he flew the F-14, F/A-18 and A-7 Corsair II aircraft.