Bring a large pot of salted water to a rolling boil. Add the rigatoni pasta and cook until just shy of al dente, according to package instructions. Drain and set aside.

In a large skillet, heat the olive oil over medium heat. Add the finely chopped onion and cook until translucent, approximately 5 minutes. Add the minced garlic and sauté for an additional 1 minute, stirring frequently to prevent burning.

Incorporate the Italian sausage (or ground beef), breaking it apart with a wooden spoon. Cook until browned and no longer pink, about 8 minutes.

Stir in the crushed tomatoes, tomato paste, dried oregano, dried basil, red pepper flakes (if using), sugar, salt, and black pepper. Reduce heat and allow the sauce to simmer for 10–15 minutes, stirring occasionally to prevent sticking. Adjust seasoning as needed.

In a medium-sized mixing bowl, combine ricotta cheese, grated Parmesan cheese, one cup of shredded mozzarella cheese, the egg, and ground nutmeg. Stir until all ingredients are fully incorporated.

Preheat the oven to 375°F (190°C). Lightly grease a 9×13-inch (23×33 cm) baking dish.

Spread a thin layer of meat sauce over the bottom of the prepared baking dish. Toss the cooked rigatoni pasta with the remaining meat sauce until evenly coated. Spread half of the pasta mixture into the baking dish.

Evenly distribute the ricotta cheese mixture over the first pasta layer. Add the remaining pasta mixture on top and spread evenly. Sprinkle the remaining one cup of shredded mozzarella cheese over the top.

Cover the baking dish with aluminum foil and place in the preheated oven. Bake for 20 minutes. Remove the foil and continue baking for an additional 10–15 minutes, or until the cheese is golden brown and bubbling.

Allow the dish to rest for 5–10 minutes before serving. Garnish with finely chopped fresh parsley and additional grated Parmesan cheese if desired. Serve warm.