Bring water to boil in a large pot and cook pasta according to package directions. Drain and set aside.

Preheat oven to 350F.

In an oven-safe skillet or cast iron pan, melt butter over low heat and add flour. Stir together and cook for about one minute.

Add milk, whisking constantly, until no visible clumps remain and the sauce is thickened. Add cheese (reserving half a cup) and stir until it is melted into the sauce. Stir in pumpkin puree, nutmeg, salt, and pepper.

Add the cooked pasta and mix well. Sprinkle reserved cheese evenly on top. Bake for 30-40 minutes until the cheese is bubbly and the top is slightly brown. Serve warm.