Preheat your oven to 400°F (200°C). Bring a large pot of salted water to a boil.

Add the pasta and cook for 2 minutes less than the package directions for al dente. Drain and set aside. (The pasta will finish cooking in the oven.)

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

Add the garlic and cook until fragrant, about 30 seconds. Stir in the crushed tomatoes, oregano, red pepper flakes (if using), 1/2 teaspoon salt, and a few grinds of black pepper. Simmer for 5 minutes, stirring occasionally.

In a large bowl, combine the drained pasta, the tomato sauce, half the mozzarella, and half the pepperoni. Stir well to coat.

Transfer the mixture to a 9x13-inch baking dish. Spread evenly. Top with the remaining mozzarella, pepperoni, and a sprinkle of Parmesan.

Cover with foil and bake for 15 minutes. Remove the foil and bake for another 10 minutes, until the cheese is bubbly and golden brown in spots.

Let rest for 5 minutes. Garnish with fresh basil or parsley before serving.