Heat oven to 350°F. Fit pie crust into 9-inch pie plate.
Heat butter in small skillet over medium heat. Add the onions and cook, stirring occasionally, until soft, 5 to 7 minutes. Stir in the thyme. Set aside.
In medium bowl, mix heavy cream, eggs, nutmeg, salt and pepper; set aside.
Layer Swiss cheese slices, crumbled bacon, bacon, onion, and spinach over the pie crust. Pour egg mixture over top. Sprinkle shredded cheddar over the top. Arrange tomato slices over the top.
Bake 40 to 50 minutes or until knife inserted in center comes out clean. Cool for at least 20 min. Cut into wedges.