Preheat oven to 350°F (177°C). With a fork, poke holes in pie crust and bake for 15 minutes. Remove pie crust but leave oven on.
Heat a skillet over med-high heat. Slice bacon crossways into ¼" pieces and fry without oil until crispy. Spoon into a bowl. In same pan, cook mushrooms flat until browned, turn and brown other side. Spoon into same bowl. In same pan, cook onions with thyme until soft. Spoon into same bowl and mix.
In a separate bowl, whisk together the eggs, cream, mustard, nutmeg, salt and pepper. Stir-in onion/bacon/mushroom mixture.
Sprinkle the cheese over the bottom of the pie shell. Pour egg mixture over that and bake for approximately 40-45 minutes until set. Sit 10 minutes and serve.