Bring a large pot of water to boil for pasta.
Preheat oven to 375-degrees.
Wash spinach and drain well. Remove stems. Cook in a pot, just until tender and wilted. Drain and squeeze out any remaining water. Chop and set aside.
In a large skillet, heat the oil, and sauté the onion and garlic for about 5 minutes. Stir in the thyme, basil, oregano and salt and pepper to taste, and the sliced mushrooms. Cook for about another 5 minutes. Add ground beef and cook until no longer pink. Remove from heat and drain any excess fat from pan. Add the spinach to the pan.
Cook pasta and drain. In a medium pan, melt butter. Stir in flour. Slowly pour in milk while stirring over medium heat. Reduce heat and simmer, stirring, for about 10 minutes until thick. Remove from heat and stir in 1 cup cheese, salt, pepper and nutmeg. Mix this cheese sauce together with the pasta until combined.
Spoon half of the pasta into a 3 quart casserole dish. Top with the meat mixture and then the remaining pasta. Sprinkle the remaining 1 cup of cheese over the top. Bake at 375-degrees for 25-30 minutes.