Boil the pasta: Bring a large pot of well-salted water to a rolling boil. Add penne and cook until just al dente, usually 1 minute less than the package suggests.
Reserve 1/2 cup pasta water, then drain.
Sauté aromatics: While the pasta cooks, warm olive oil in a large skillet over medium heat. Add onion with a pinch of salt and cook 4–5 minutes until translucent. Stir in garlic and cook 30 seconds, just until fragrant.
Build the sauce: Pour in crushed tomatoes.
Add red pepper flakes and oregano. Simmer 5–7 minutes, stirring occasionally, until slightly thickened. Season with salt and pepper.
Adjust the texture: Stir in a splash of the reserved pasta water to loosen the sauce to a silky, clinging consistency.
Add butter if using for extra gloss.
Combine: Add drained penne to the skillet. Toss over low heat for 1–2 minutes so the pasta absorbs the sauce. Add more pasta water as needed.
Finish: Off the heat, fold in Parmesan until melted and creamy.
Taste and adjust seasoning. Sprinkle with chopped basil or parsley.
Serve: Plate hot with extra cheese on top. Add any optional proteins or veggies in step 5 to warm through before finishing with cheese.