Preheat your oven to 375°F. Lightly grease a 9x13-inch baking dish. Get a large pot of well-salted water boiling.

Bring a large pot of salted water to a boil. Cook the rigatoni until just al dente. Before draining, reserve about 1/2 cup pasta water.

While the pasta cooks, heat the olive oil in a large skillet over medium heat. Add the onion and cook until softened, about 3–4 minutes.

Stir in the garlic and cook for 30 seconds.

Add the ground beef and cook until browned, breaking it up as it cooks. Drain excess grease if needed.

Stir in the marinara, tomato paste, Italian seasoning, salt, pepper, and red pepper flakes if using. Simmer for 3–5 minutes.

Add the drained pasta to the sauce and toss to coat. Stir in 1 cup mozzarella. Add a splash of reserved pasta water if it looks tight.

Transfer everything to the prepared baking dish. Top with the remaining 1 cup mozzarella and the Parmesan.

Bake for 20–25 minutes, until hot and bubbly and the cheese is melted. Broil for 1–2 minutes at the end if you want extra color.

Let it rest for 5–10 minutes, then serve.