Chicken, butternut squash, and spinach skillet pasta bake

We had the hugest butternut squash I have even seen. It came from my father-in-law's garden and was just really massive. We used 1/3 of it to make a side dish for Thanksgiving (that produced leftovers) - that's how big it was. 

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So, needless to say, we've been eating a lot of butternut squash. I threw this pasta dish together using a lot of leftovers -- more of the squash, some chicken, a hunk of mozzarella, etc. It was a really satisfying and tasty pasta dish and was a perfect meal for a cold and snowy evening. 

This dish will feed about 4-6 people, so we had a lot of lunch leftovers (my favorite).

Chicken, butternut squash, and spinach skillet pasta bake
1 lb. short-cut pasta 
3 tablespoons butter, divided
1 shallot, minced
1 garlic clove, minced
1 large chicken breast, diced (about 1-1/4 cups)
about 3 cups peeled and diced butternut squash
1/8 teaspoon cayenne pepper
1/2 teaspoon freshly grated nutmeg
sea salt and freshly ground black pepper, to taste
2 tablespoons all-purpose flour
3 cups milk
1/3 cup plus 2 tablespoons, freshly grated Parmesan cheese
4 packed cups baby spinach
1-1/2 cups grated mozzarella cheese

Preheat the oven to 400 degrees. Start a large pot of salted water to boil for cooking the pasta. When it boils, cook the pasta until it is a couple minutes short of al dente and then drain and set aside.

In an oven-proof skillet, heat 1 tablespoon of butter over medium heat. Add the shallot and cook for about 1-2 minutes. Stir in the garlic, chicken, and butternut squash. Let cook, stirring often, until the chicken is cooked through and the squash is fork tender. Stir in the cayenne pepper, nutmeg, salt, and pepper and cook until just fragrant. Turn off the heat.

While the chicken/squash are cooking, make the sauce. In a medium saucepan, melt the remaining 2 tablespoons of butter. Whisk in the flour and cook for about 2-3 minutes. Then whisk in the milk until no lumps remain. Continue to cook, whisking often, until the milk begins to thicken, about 15 minutes. Once it thickens, remove from the heat, stir in the 1/3 cup of Parmesan, along with a pinch of salt and a couple grinds of pepper.

Gently stir the cooked pasta and spinach into the skillet and then stir in the sauce. Top with the mozzarella and the remaining 2 tablespoons of Parmesan. Transfer the skillet to the oven and bake until the cheese is melted and bubbly, about 10-12 minutes.