Preheat your oven to 375°F (190°C) and grease a 9x13-inch baking dish.

Cook the rigatoni pasta in salted boiling water for 1-2 minutes less than package instructions to achieve al dente.

In a skillet, heat olive oil and sauté chopped onion until translucent, then add minced garlic and cook until fragrant.

Add ground beef to skillet, breaking it apart as it cooks until browned; season with oregano, basil, salt, pepper, and red pepper flakes.

Stir in tomato paste, marinara sauce, and water; simmer for 10-15 minutes until it thickens.

In a mixing bowl, combine cooked rigatoni, two-thirds of the meat sauce, half of the mozzarella, and all Parmesan cheese.

Pour mixture into the baking dish, top with remaining meat sauce and sprinkle the rest of the mozzarella cheese.

Cover with foil and bake for 20 minutes, then remove foil and bake for 10-15 more minutes until top is golden.

Allow to rest for 10 minutes before serving; garnish with fresh parsley or basil.