Place the bacon into a skillet, and cook over medium heat until browned. Remove bacon from skillet, reserving 4 tablespoons bacon fat, and drain on paper towels.
Place the onions into the same skillet with the bacon fat, and cook over medium-high heat until evenly browned, about 8 minutes. Season with salt and pepper. Combine the milk and cream in a bowl. Sprinkle the flour over the onions, and stir to blend. Stir in the milk mixture. Cook and stir over medium heat until the mixture thickens. Remove from heat, stir in the bacon, and set aside to cool 10 minutes.
Beat the eggs in a mixing bowl until light colored and frothy. Stir a spoonful of the onion mixture into the eggs. Add another spoonful of the onion mixture, and continue stirring. Repeat, until all the onions have been stirred into the eggs and are thoroughly blended. Pour the mixture into the prepared pie shell. Sprinkle with nutmeg.
Bake in preheated oven until the crust is lightly browned, about 20 minutes. Remove from the oven and cool 5 minutes before serving.