Roast the squash. Preheat the oven to 400°F (204°C). Toss the butternut squash with olive oil, salt, black pepper, smoked paprika, sage, and thyme.
1 small butternut squash, 1 tablespoon olive oil, 1 teaspoon kosher salt, ½ teaspoon black pepper, ½ teaspoon smoked paprika, 3 to 4 fresh sage sprigs, 2 to 3 fresh thyme sprigs
Spread in a single layer on a parchment-lined baking sheet. Roast for 25 to 30 minutes, until tender and caramelized.
Reserve about 1 cup of roasted squash for folding into the pasta. Blend or mash the remaining squash until smooth, about 1 cup of puree.
Cook the pasta. Bring a large pot of salted water to a boil. Cook the pasta according to package directions until al dente, or 1 minute less than al dente. Drain and set aside.
12 oz pasta
Brown the butter and crisp the sage. Melt the butter in a large pot or rondeau style deep skillet over medium heat. Add the sage leaves and cook for 2 to 3 minutes, swirling occasionally, until the butter is golden brown and smells nutty. Remove the crispy sage leaves and reserve them for garnish.
4 tablespoons butter, 8 to 10 fresh sage leaves
Make the roux. Whisk the flour into the brown butter. Cook for 1 to 2 minutes, whisking constantly, until bubbly and lightly golden.
2 tablespoons all-purpose flour
Build the sauce. Slowly whisk in the whole milk and heavy cream. Continue whisking for 3 to 4 minutes, until smooth and slightly thickened.
2 cups whole milk, ½ cup heavy cream
Add the squash and seasonings. Stir in the butternut squash puree, Dijon mustard, garlic powder, smoked paprika, nutmeg, salt, and black pepper. Stir until smooth and creamy.
1 tablespoon Dijon mustard, 1 teaspoon garlic powder, ½ teaspoon smoked paprika, ½ teaspoon ground nutmeg, Kosher salt and black pepper
Melt in the cheese. Reduce the heat to low. Add the sharp white cheddar, Gruyère, and Parmigiano-Reggiano. Stir gently until the cheese is melted and the sauce is smooth and velvety. Taste and adjust the seasoning as needed.
1 ½ cups sharp white cheddar, 1 cup Gruyère, ¼ cup Parmigiano-Reggiano
Combine. Add the cooked pasta and toss until evenly coated. Gently fold in the reserved roasted butternut squash cubes.
Transfer to the baking dish. Reduce the oven temperature to 375°F (190°C). Lightly butter a 9 x 13-inch baking dish. Spoon in the mac and cheese and spread evenly.
Add the topping. Sprinkle the sharp cheddar and Parmigiano-Reggiano evenly over the top.
½ cup sharp cheddar
Bake until bubbly. Cover with foil and bake for 10 minutes. Remove the foil and bake for another 10 to 15 minutes, until the cheese is melted, the edges are bubbling, and the top is lightly golden.
Finish and serve. Let rest for 5 minutes. Garnish with the crispy sage leaves and freshly cracked black pepper before serving.