Preheat oven to 400°F. Prick bottom and sides of shell with a fork and bake shell for 10 minutes. Allow to cool for approximately 10 minutes and reduce oven temperature to 350°F.

Meanwhile, make the filling: Combine the butter, onions and a big pinch of salt in a medium skillet over low heat. Cook, stirring occasionally, until the onion is very tender and golden brown, 20 to 25 minutes. While the onion cooks, put the bacon in a small nonstick skillet over medium heat and cook, stirring occasionally, until golden brown and crisp, 7 to 10 minutes. Remove to a paper towel–lined plate. Add the bacon to the pan with the onion, along with the thyme.

Place asparagus in a steamer over 1 inch of boiling water, and cover. Cook until tender but still firm, about 2 to 6 minutes. Drain and cool.

Spread the Gruyère and onion-bacon mixture in the cooled pie crust. Combine the remaining ingredients with 3/4 teaspoon salt in a large bowl and whisk until combined. Pour into the pie crust. Bake until the quiche is just set and lightly golden brown, 40 to 45 minutes. Let cool before serving.