Preheat oven to 350°F. Lightly coat a 13x9-inch baking dish with vegetable cooking spray.
Bring a large pot of water to a boil and cook pasta al dente according to package directions. Drain the pasta then put it back in the warm pot. Add the spinach leaves to the pasta and gently toss or stir to combine. The leaves should wilt a little once they sit in the hot pasta. Set aside, stirring occasionally while mixing the cheese together.
In a medium mixing bowl combine the ricotta, cottage cheese, beaten egg, garlic, nutmeg, red pepper flakes, salt, pepper, parsley, basil, Parmesan cheese and 1 cup of the Mozzarella. Fold together until blended. Add a little more than half the cheese mixture to the pasta and spinach. Mix gently using a rubber spatula or large wooden spoon.
Pour 1 cup of the marinara sauce into the bottom of the prepared pan and spread to cover. Pour the pasta and spinach mixture into the pan and then top with dollops of the remaining ricotta mixture. Spread the remaining marinara over the top. Cover the pan lightly with foil and bake for 20 minutes. Remove the foil and top with the remaining Mozzarella cheese. Continue baking (uncovered) until the dish is hot and bubbly and the cheese melted and lightly browned, about 20-25 minutes more.
Serve with additional Parmesan and fresh parsley if desired.