In 1988, Stott joined NASA at the Kennedy Space Center (KSC), Florida as an Operations Engineer in the Orbiter Processing Facility (OPF). After six months, she was detailed to the Director of Shuttle Processing as part of a two-person team tasked with assessing the overall efficiency of Shuttle processing flows, and implementing tools for measuring the effectiveness of improvements. She was the NASA KSC Lead for a joint Ames/KSC software project to develop intelligent scheduling tools. The Ground Processing Scheduling System (GPSS) was developed as the technology demonstrator for this project. GPSS was a success at KSC, and also a commercial success that is part of the PeopleSoft suite of software products. During her time at KSC, Stott also held a variety of positions within NASA Shuttle Processing, including Vehicle Operations Engineer; NASA Convoy Commander; assistant to the Flow Director for Space Shuttle Endeavour; and Orbiter Project Engineer for Columbia. During her last two years at KSC, she was a member of the Space Station Hardware Integration Office and relocated to Huntington Beach, California where she served as the NASA Project Lead for the ISS truss elements under construction at the Boeing Space Station facility. In 1998, she joined the Johnson Space Center (JSC) team in Houston, Texas as a member of the NASA Aircraft Operations Division, where she served as a Flight Simulation Engineer (FSE) on the Shuttle Training Aircraft (STA).