Cook the penne pasta according to package instructions in a large pot of salted boiling water until al dente. Drain and set aside, reserving 1/2 cup of pasta water.
In a large skillet, heat the olive oil over medium heat. Add the chopped onion and sauté until translucent, about 5 minutes.
Stir in the minced garlic and red pepper flakes, cooking for an additional minute until fragrant.
Pour in the tomato sauce and bring to a simmer. Cook for 5 minutes, allowing the flavors to meld.
Reduce the heat to low and stir in the heavy cream and Parmesan cheese. Mix until the cheese has melted and the sauce is creamy.
Add the cooked penne pasta to the skillet, tossing to coat the pasta in the sauce. If the sauce is too thick, add reserved pasta water a little at a time until desired consistency is reached.
Season with salt and pepper to taste. Serve hot, garnished with fresh basil leaves.