Step 1: Prepare the Pasta

1. Bring a large pot of salted water to a boil. Add the penne pasta and cook until al dente, following package instructions. This should take around 8-10 minutes. Drain the pasta and set aside, reserving ½ cup of the pasta water.

Step 2: Make the Alfredo Sauce

2. In a large skillet or saucepan, melt the unsalted butter over medium heat. Add the minced garlic and sauté for 1-2 minutes until fragrant, making sure not to burn the garlic.
3. Pour in the heavy cream and whole milk, stirring well to combine. Let the mixture simmer gently for 5-7 minutes, stirring occasionally until it begins to thicken slightly.
4. Stir in the grated Parmesan cheese, salt, ground black pepper, and a pinch of nutmeg. Continue cooking until the cheese melts and the sauce thickens to your desired consistency. Remove from heat and set aside.

Step 3: Combine the Pasta and Sauce

5. Preheat your oven to 375°F (190°C).
6. In a large mixing bowl, combine the cooked penne pasta with the Alfredo sauce. Stir in the chopped spinach and basil, ensuring the sauce coats the pasta evenly and the greens are well-distributed.

Step 4: Layer the Cheese

7. In a separate bowl, mix together the shredded mozzarella cheese, ricotta cheese, and crumbled feta cheese. Fold half of this cheese mixture into the pasta, stirring to combine.
8. Transfer the pasta and sauce mixture into a greased 9×13-inch baking dish. Spread it out evenly, and then top with the remaining cheese mixture, followed by the additional 1 cup of shredded mozzarella and ½ cup grated Parmesan for an extra cheesy crust.

Step 5: Bake to Perfection

9. Cover the baking dish with aluminum foil and bake in the preheated oven for 20 minutes.
10. Remove the foil and continue baking for another 10-15 minutes or until the top is bubbly and golden brown.
11. Once baked, let the dish rest for 5-10 minutes before serving. Garnish with fresh basil leaves and a sprinkle of red pepper flakes if desired.