Bring a large pot of salted water to a boil and cook the ziti until just al dente, about 8 minutes. Drain and toss with a splash of olive oil to prevent sticking.
While the pasta cooks, heat olive oil in a skillet over medium heat. Sauté chopped onions and minced garlic until they become fragrant and translucent, about 2-3 minutes, filling the kitchen with a savory aroma.
Add marinara sauce and red pepper flakes to the skillet. Simmer the mixture for 10 minutes, allowing the flavors to meld and the sauce to thicken slightly, releasing a rich, spicy scent.
In a large mixing bowl, combine the cooked pasta with the sauce mixture and half of the shredded mozzarella cheese. Mix gently until evenly coated and cheese is well distributed.
Transfer the pasta mixture to a baking dish, spreading it out evenly. Top with the remaining mozzarella cheese and sprinkle grated Parmesan over the top for added flavor and a golden crust.
Preheat your oven to 375°F (190°C). Bake the ziti for 20-25 minutes until bubbling around the edges and the cheese on top is melted and golden brown, filling your kitchen with a tempting aroma.
Remove the dish from the oven and let it rest for 5 minutes so the cheese can set slightly, making it easier to serve. Garnish with fresh basil or parsley if desired, for a burst of color and freshness.
Serve hot and enjoy the bubbling, cheesy, smoky flavors of this hauntingly delicious baked ziti—perfect for a cozy night or a spooky gathering.