Cube the cheese. Cook the macaroni while preparing the cheese sauce. Sauté onion in butter until soft and transparent. Add the flour and pepper, cooking for 1 minute, stirring constantly. Add the milk slowly, continuously stirring. This may be done in several batches. Cook over medium heat until the mixture thickens. Add the cheese gradually and stir constantly until all of the cheese is melted. Drain macaroni and pour cheese sauce into pot. Stir well. Pour into a 13 x 9 baking pan that has been sprayed with Pam. Bake at 375 degrees for 30 minutes.