1. Preheat your oven to 400°F (200°C). Line a baking sheet with parchment paper. Toss the cubed butternut squash and diced onion with a drizzle of olive oil, salt, and pepper. Spread them in a single layer on the prepared baking sheet. Roast for 25–30 minutes, or until the squash is tender and lightly caramelized.

2. While the squash is roasting, cook the pasta in a large pot of salted boiling water according to package directions until al dente. Drain the pasta and set it aside.

3. Transfer the roasted butternut squash and onion to a blender. Add the minced garlic and 1/2 cup of the milk. Blend until the mixture is smooth and creamy.

4. In a large saucepan, melt 2 tablespoons of butter over medium heat. Add the all-purpose flour and whisk continuously for 1 minute to create a smooth roux.

5. Gradually whisk in the remaining 1 1/2 cups of milk, stirring constantly until the sauce thickens to a smooth consistency, about 3–5 minutes.

6. Stir the blended butternut squash mixture into the thickened sauce. Add the ground nutmeg and dried thyme (if using). Season with salt and pepper to taste.

7. Reduce the heat to low. Add the shredded cheddar, Gruyère, and Parmesan cheeses to the sauce. Stir gently until melted and smooth.

8. Gently add the cooked pasta to the cheese sauce, stirring carefully to coat evenly.

9. Pour the pasta and cheese mixture into a lightly greased 2-quart baking dish.

10. In a small bowl, combine the panko breadcrumbs with the melted butter. Sprinkle evenly over the top of the pasta in the baking dish.

11. Bake in the preheated oven at 400°F (200°C) for 10–15 minutes, or until the mac and cheese is bubbly and the topping is golden brown.

12. Garnish with chopped fresh parsley just before serving, if desired.