Cook the ziti pasta according to package instructions until al dente. Drain and set aside.
In a large skillet over medium heat, add the olive oil. Once hot, add the chopped onion and minced garlic. Sauté for 3-4 minutes until softened.
Add the ground beef or turkey to the skillet. Cook until browned, breaking it apart as it cooks. Drain excess fat if necessary.
Stir in the marinara sauce, diced tomatoes, Italian seasoning, red pepper flakes, salt, and pepper. Let simmer for about 5-7 minutes.
In a separate bowl, mix together the ricotta cheese, cottage cheese, and half of the mozzarella cheese. Season with a bit of salt and pepper.
In a large mixing bowl, combine the cooked ziti pasta with the meat sauce mixture until well coated.
In a greased 9x13-inch baking dish, spread half of the ziti mixture evenly at the bottom. Dollop spoonfuls of the cheese mixture on top. Layer the remaining ziti mixture over it.
Sprinkle the top with the remaining mozzarella and all the Parmesan cheese.
Cover with aluminum foil and bake for 20 minutes. Remove the foil and bake for an additional 15-20 minutes or until bubbly and golden on top.
Allow to cool slightly before serving. Garnish with fresh basil leaves.