Step 1

Set a large, wide, deep-sided skillet or pot over medium heat. Melt 2 tablespoons butter and add the onions. Cover the skillet or pot (use foil, if needed), and cook for 5 minutes. Uncover, turn heat to medium-low, and add 1/2 teaspoon each salt and pepper, 4 sprigs thyme, and bay leaves. Cook, stirring frequently, for 40 - 60 minutes, or until onions are a deep caramel hue and sweet-tasting. Onions can be caramelized ahead and kept in the fridge until needed.

Step 2

While onions cook, preheat oven to 425 degrees F. Butter a 9 x 13-inch baking dish.

Step 3

Once the onions have caramelized, remove thyme sprigs and bay leaves. Turn heat up to medium, add 2 tablespoons butter and 1/2 teaspoon salt. Sprinkle flour over the onions and cook, stirring constantly for 2 minutes. Stirring often, gradually add the milk in half cup increments, bringing roux to a gentle simmer between additions. Keep adding milk and stirring until mixture has thickened, about 25 minutes.

Step 4

Meanwhile, cook pasta, drain, and tip into prepared baking dish.

Step 5

Remove skillet or pot from heat and fold grated cheese into the roux (reserve 1/4 cup grated cheese for topping). Pour cheese mixture over the pasta and gently toss.

Step 6

In a small bowl, combine the remaining tablespoon of butter with the panko and cheese. Smush the butter into the panko with your fingertips. Add a pinch each salt and pepper. Sprinkle panko mixture over top of the mac.

Step 7

Mac can be prepped up to this point, covered and refrigerated for 3 days. Give it 30 minutes to come to room temp before baking.

Step 8

Slide mac and cheese into the oven and bake until top is golden and filling is very bubbly, about 25 minutes. If desired garnish with thyme sprigs or leaves.