Cook pasta according to package instructions. SUBTRACT 3 minutes from the recommended boiling time. This will prevent the pasta from becoming mushy later.
Preheat the oven to 400°. Line a large baking sheet with aluminum foil.
Making Butternut Squash Puree
Place diced butternut squash in a large bowl and season olive oil, salt, pepper, and nutmeg. Toss and make sure the pieces are evenly coated.
Transfer butternut squash onto a baking sheet and roast for 25-30 minutes. Once you've done reduce the heat to 350°.
Transfer the roasted butternut squash into a food processor and add vegetable broth. Blend until the butternut squash until creamy. Set aside.
Making the Cheese Sauce
In a large sauté pan melt butter over medium-low heat, add flour and stir until the butter and flour have created a paste (roux).
Slowly pour milk into the mixture. Stir frequently until the milk has warmed and the mixture has thickened. About 7-10 minutes. Season with salt, pepper, and dry mustard. Add ¾ of Cheddar cheese to the sauce. and simmer for a couple of minutes.
Add cooked pasta to the cheese sauce and transfer everything into a large baking dish. Top with the remaining Cheddar cheese.