Following this period of time, McDonald held a number of academic posts at Pennsylvania State University and Mississippi State before accepting an Interagency Personnel Appointment at NASA where he was the Center Director at NASA Ames Research Laboratory from 1996 to 2002. During his stay at NASA, McDonald led an Aeromechanical Team investigation of a V-22 Osprey accident, reporting to the Assistant Secretary of Defense. At the request of a NASA administrator, McDonald then led a special investigation into space shuttle mishaps and this preceded the Space Shuttle Columbia disaster. This particular investigation identified many of the systemic issues later cited by the Columbia Accident Investigation Board. During his tenure McDonald also initiated the University Affiliated Research Center, the NASA Research Park, and the Space Science and Astrobiology Division.