Bring a large pot of salted water to a boil. Add the penne or rigatoni and cook according to package instructions until al dente. Drain and set aside.
Heat 2 tablespoons of olive oil over medium heat in a large skillet. Add the spicy chicken sausage, breaking it up with your spoon, and cook until browned and cooked through, about 5-7 minutes. Remove excess fat if necessary. Then add the diced onion, red bell pepper, and green bell pepper. Sauté until the vegetables soften, about 5 minutes. Stir in the minced garlic and red pepper flakes, cooking for another minute until fragrant.
Pour in the crushed tomatoes and sprinkle the Italian seasoning. Stir well to combine. Season with salt and pepper to taste. Let the sauce simmer gently for 10 minutes to meld the flavors.
Add the cooked pasta to the skillet with the sausage and pepper sauce. Stir until every piece of pasta is well coated.
Preheat your oven to 375°F (190°C). Transfer the pasta mixture to a greased 9x13 inch baking dish. Sprinkle the shredded mozzarella and grated Parmesan evenly over the top.
Bake uncovered for 20-25 minutes, or until the cheese is melted and bubbly with golden spots. Remove from the oven and let it rest for a few minutes before serving. Garnish with fresh basil if desired.