In a large pot over medium heat, bring about 4 quarts water to a boil. Add pasta and cook for about 1 to 2 minutes less than package directions.
Add spinach at the last 30 seconds of cooking. Drain noodles and spinach.
While the pasta is cooking, heat a saucepan over medium heat. Add bacon and cook, stirring regularly, until crisp. With a slotted spoon, remove from pan.
Add flour to the bacon drippings and cook, stirring regularly, for about 1 to 2 minutes or until bubbly.
Gradually add milk, whisking vigorously to prevent lumps. Bring to a simmer, whisking constantly, for about 3 to 5 minutes or until thickened.
Add Parmesan cheese, 1 cup of the cheddar cheese. Continue to cook, whisking constantly. for about 2 to 3 minutes or until melted.
Add cayenne pepper and nutmeg. Season with salt and pepper to taste. Remove from heat.
Add pasta-spinach mixture and 2/3 of the bacon to the cheese sauce and stir gently to combine.
Lightly grease a casserole with cooking spray. Spoon pasta mixture into casserole. Top with the remaining 1/3 of the bacon and the remaining 1 cup cheddar cheese.
Bake in a 350 F oven for about 15 to 20 minutes or until heated through and cheese is melted.
Remove from oven and allow to rest for about 5 minutes before serving.