1/4teaspoonfreshly ground black pepper, plus more to taste
For the breadcrumb topping:
1 1/2tablespoonschopped fresh sage
1tablespoongrated Parmesan cheese
2tablespoonsmelted unsalted butter
Freshly ground black pepper
Cook pasta in a large pot of salted, boiling water, and drain 2 minutes shy of the package instructions. Transfer to a large bowl and set aside. Preheat an oven to 375°F and set an oven rack in the middle position.
Melt butter in a large skillet over medium heat, then add the onion, garlic, thyme leaves and a pinch of salt. Cook, stirring occasionally, until onions are soft (about 5 minutes). Stir in the flour and cook for 3 minutes, then stir in the milk and cook until just starting to thicken (about 3 minutes). Take the sauce off the heat, then stir in the cheddar until fully incorporated. Add butternut squash, mustard, nutmeg, cayenne and black pepper, stirring to combine. Season to taste with kosher salt.
Pour cheese sauce into the bowl with the cooked shells until the macaroni is sufficiently coated in sauce. You may not use all the sauce (I had a little leftover). Using a spatula, transfer shells and sauce into a 9" x 13" baking dish.
Combine breadcrumbs, sage, Parmesan cheese and melted butter in a medium bowl, tossing until crumbs are evenly coated in the butter. Season with a pinch of kosher salt and several turns of black pepper. Sprinkle breadcrumb topping evenly over the shells and cheese. Bake in the oven until the breadcrumbs are golden brown and sauce bubbles around the edges (25 - 30 minutes). Let cool for a few moments before serving.
* This mac and cheese can be prepared up to a day in advance up to step 3. Cover and store in the refrigerator until ready to bake. Let come to room temperature then continue on with step 4.