Preheat the oven to 375°F (190°C). Grease a 9×13-inch baking dish and bring a large pot of salted water to a boil.

Cook the rigatoni 2 minutes shy of package directions so the pasta remains al dente after baking. Drain and set aside.

While pasta cooks, heat olive oil in a large skillet over medium-high heat. Add the chopped onion and sauté until translucent, about 4 minutes.

Add the ground beef and cook until browned, breaking it into bite-size pieces. Season with salt, pepper, oregano, and red pepper flakes if using. Drain excess fat if needed.

Stir in the minced garlic and cook for 30 seconds until fragrant. Pour in the marinara sauce and simmer gently for 5 minutes to let flavors meld.

In a large bowl, combine the cooked rigatoni, meat sauce, and ricotta. Stir gently until everything is coated and creamy. Taste and adjust seasoning.

Spoon half the pasta mixture into the prepared dish. Sprinkle half the mozzarella and half the Parmesan over the layer. Add the remaining pasta and top with remaining cheeses.

Bake uncovered for 20 minutes, then broil for 2 to 3 minutes to create a golden, bubbly top—watch closely so it does not burn.

Remove from the oven and let rest for 5 minutes before serving so the pasta sets and slices hold together.