Heat the olive oil in a large oven-safe skillet over medium-heat. Stir in the onions with a big pinch of salt. Cook over medium, stirring often, until the onions soften, about 10 to 15 minutes.

Decrease the heat to low or medium-low. Cook the onions, stirring often, for about 60 to 90 minutes, until they are golden and caramelly. If at any time the onions start to burn, low the heat or add a few splashes of water to keep them hydrated.

Preheat the oven to 375 degrees F. Boil the pasta according to the package directions.

Once the onions are golden and caramelly, transfer them to a plate. (Note: if you’re really in a rush, you can add 1 teaspoon of sugar, honey, maple syrup, etc to speed along the caramelization process. Be sure to stir often and check on the progress!)

Add the butter to the skillet. Once melted, add in the flour, whisking to create a roux. Cook for 2 to 3 minutes, until it becomes golden in color and starts to smell nutty. Slowly stream in the milk while stirring constantly. The mixture will begin to come together and thicken. Stir in the nutmeg.

Stir in almost all of the cheese (reserve a bit for topping) until it is melted. Add in ¾ of the caramelized onions. Stir in the pasta. Toss it together over and over until it is combined.

Top with the remaining cheese on top along with the remaining onions. Sprinkle with the bread crumbs. Bake for 25 to 30 minutes, or until golden and bubbly.

Remove and sprinkle with fresh thyme. Serve!