Morgan was born in Syracuse, New York, and moved to El Cajon, California at the age of 14.
While attending El Cajon Valley High School, he met James Wong, who would become his friend and professional partner. Both enrolled at Loyola Marymount University, graduating from the School of Film and Television in 1983, and afterward, wrote many scripts together.
Morgan did not want to work on television at first, but wound up accepting a job on 21 Jump Street, which would later earn he and Wong a steady job at Stephen J. Cannell Productions. As Morgan was about to leave the company following scripts for The Commish in 1992, his former boss at Cannell, Peter Roth, invited him to work on a show being developed at 20th Television, The X-Files.