Step 1: Preheat oven to 375°F (190°C) and grease a 9×13 inch baking dish.
Step 2: Cook ziti pasta according to package directions until al dente, then drain and set aside.
Step 3: In a large skillet, heat olive oil over medium heat and sauté onion until translucent, about 5 minutes.
Step 4: Add garlic and ground beef to the skillet, breaking up the meat with a spoon, and cook until browned, about 8-10 minutes.
Step 5: Stir in crushed tomatoes, tomato sauce, oregano, basil, red pepper flakes (if using), salt, and pepper. Simmer for 15 minutes.
Step 6: In a large bowl, combine cooked ziti, meat sauce, ricotta cheese, and half of the mozzarella and Parmesan cheeses.
Step 7: Transfer the mixture to the prepared baking dish and top with remaining mozzarella and Parmesan cheeses.
Step 8: Bake uncovered for 25-30 minutes until bubbly and cheese is golden brown.
Step 9: Let cool for 5 minutes, garnish with fresh basil, and serve warm.