Bring a large pot of salted water to a boil. Add the ziti and cook according to package instructions until al dente, usually about 9-11 minutes. Drain and set aside.
While the pasta cooks, heat olive oil in a large skillet over medium heat. Add diced onion and sauté for about 3-4 minutes until translucent. Stir in minced garlic and cook for another 30 seconds until fragrant.
Add the ground beef or turkey to the skillet. Break it apart with your spoon and cook until browned and no longer pink, about 6-8 minutes. Drain any excess fat if necessary.
Pour in the fire-roasted crushed tomatoes, then stir in dried basil, oregano, red pepper flakes (if using), salt, and pepper. Bring the sauce to a simmer and let it cook for 10-15 minutes, stirring occasionally, to let the flavors meld.
In a large mixing bowl, combine the cooked ziti with the marinara sauce and half of the shredded mozzarella. Stir gently to coat the pasta evenly.
Preheat your oven to 375°F (190°C). In your baking dish, spread half of the pasta-sauce mixture evenly. Dollop half of the ricotta cheese over the pasta and sprinkle with a bit of Parmesan. Repeat with the remaining pasta, ricotta, and Parmesan.
Finish by sprinkling the remaining mozzarella cheese evenly over the top.
Bake uncovered for 25-30 minutes, or until the cheese is melted and bubbly with golden spots on top. For an extra bubbly crust, you can broil for 1-2 minutes at the end—just watch carefully so it doesn’t burn.
Remove from the oven and let the baked ziti rest for 5 minutes before serving. This helps everything set and makes it easier to portion out.