Preheat your oven to 375°F, and grease a 9x13-inch casserole dish.
Cook the pasta according to the package instructions until al dente. Drain and set aside.
12 ounces penne pasta
In a large skillet, heat the olive oil over medium heat. Add the Italian sausage and cook until browned, breaking it up into crumbles as it cooks. Remove the sausage and set aside.
1 tablespoon olive oil, 1 pound ground Italian sausage
In the same skillet, add the diced onion and bell pepper. Sauté until softened, about 5 minutes. Add the minced garlic and cook for another minute.
1 small onion, 1 bell pepper, 3 cloves garlic
Add the marinara sauce, cooked sausage, 1 cup of mozzarella, pepperoni slices, oregano, basil, and red pepper flakes to the skillet. Stir to combine and simmer for 5 minutes.
24 ounce jar marinara sauce, 1 cup pepperoni slices, 1 teaspoon dried oregano, 1 teaspoon dried basil, ½ teaspoon red pepper flakes
Add the cooked pasta to the skillet and toss to combine with the sauce. Transfer to the prepared baking dish and sprinkle the remaining 1 cup of mozzarella and grated Parmesan cheese.
½ cup grated Parmesan cheese
Bake, uncovered, for 15-20 minutes, or until the cheese is melted and bubbly.
Garnish with fresh basil or parsley if desired and serve warm.