Cook pasta according to package instructions. SUBTRACT 3 minutes from the recommended boiling time.
Preheat the oven to 400°. Line a large baking sheet with aluminum foil.
BUTTERNUT SQUASH PUREE
Place diced butternut squash in a large bowl, season with olive oil, salt, pepper, and nutmeg, and toss until well combined.
Transfer butternut squash onto the baking sheet and roast for 25 minutes. Once done, reduce the heat to 350° Fahrenheit.
Transfer the roasted butternut squash into a food processor and add vegetable broth. Blend until the butternut squash until creamy. Set aside.
CHEESE SAUCE
In a large pot, melt butter over medium-low heat, add flour, and stir until the butter and flour have created a paste (roux).
Pour milk into the mixture. Stir until the milk has warmed and the mixture has thickened. About 5-7 minutes. Season with salt, pepper, and mustard. Add ¾ of Cheddar cheese and the creamy butternut squash to the sauce and simmer for a few minutes.
Add cooked pasta to the cheese sauce and transfer everything into a casserole dish. Top with the remaining Cheddar cheese.