Preheat the oven to 375°F and lightly grease a 9×13-inch baking dish.

Bring a large pot of well-salted water to a boil. Cook the ziti for 1–2 minutes less than the package instructions for al dente. Drain and set aside.

In a large skillet over medium heat, heat the olive oil. Add the diced onion and cook for 5–6 minutes until soft and translucent. Add minced garlic and sauté for 30 seconds.

Stir in salt, black pepper, Italian seasoning, and red pepper flakes (if using). Pour in the marinara sauce and let it simmer for 5–7 minutes.

In a large bowl, combine ricotta cheese, egg (if using), half of the Parmesan cheese, and half of the shredded mozzarella cheese. Season and mix well.

Toss the cooked pasta with marinara sauce until coated. Layer half of the pasta in the baking dish, add dollops of half the ricotta mixture, then repeat the layers.

Top with remaining mozzarella and Parmesan cheeses.

Cover loosely with foil and bake for 20 minutes. Remove foil and bake uncovered for another 10–15 minutes until bubbly and golden.

Let the dish rest for 10 minutes before serving. Garnish with basil or parsley if desired.