Melt the butter in a large skillet over medium heat. Add the onions, cover and steam until the onions are soft, stirring occasionally. Season with salt and pepper. Drain any accumulated liquid and arrange the onions in the baked pie crust. Sprinkle with cheese.
In a medium bowl, whisk together the eggs, yolks, cream and nutmeg and pour on top of the onions/cheese in the crust.
Bake for 30 minutes, or until set and puffy. Let sit for 5 minutes before cutting.