Preheat your oven to 375°F (190°C).
Bring a large pot of water to a boil. Season generously with salt—the water should taste like the sea. Add the penne and cook for 2 minutes LESS than the package directions. You want it very al dente (almost undercooked) as it will continue to cook in the oven. Drain the pasta.
Meanwhile, heat a large skillet over medium-high heat. Add a tablespoon of olive oil and the Italian sausage, breaking it into smaller pieces as it cooks. Brown for about 5-7 minutes until no longer pink.
Add the diced onion and bell pepper (if using) to the sausage. Cook for another 3-4 minutes until the vegetables have softened.
Stir in the minced garlic, Italian seasoning, and red pepper flakes (if using). Cook for another 30 seconds until fragrant. Your kitchen should smell amazing right about now.
Pour in the marinara sauce and bring to a simmer. Let it cook for about 5 minutes, stirring occasionally. Season with salt and pepper to taste, keeping in mind that the sausage and cheeses will add saltiness.
In a large bowl, combine the ricotta cheese, 1 cup of mozzarella, ¼ cup of Parmesan, and the chopped basil. Mix well.
Add the drained pasta to the cheese mixture and toss until the pasta is well coated.
Combine the pasta/cheese mixture with the sausage and sauce. You can do this directly in the skillet if it's large enough, or in the pasta pot, or even in your baking dish if you're feeling rebellious.
Transfer everything to your 9x13 inch baking dish. Top with the remaining 1 cup of mozzarella and ¼ cup of Parmesan.
Drizzle the top with the remaining tablespoon of olive oil – this helps the cheese get that beautiful golden color.
Cover with aluminum foil and bake for 20 minutes. Then remove the foil and bake for an additional 10 minutes until the cheese is bubbly and starting to brown in spots.
Let it rest for 5 minutes before serving. This allows the casserole to set slightly and makes it easier to portion. Garnish with additional fresh basil.