Bring a large pot of salted water to a boil, add the penne pasta and cook, until about three-quarters of the way done (2 minutes under what's called for on the package. 

Meanwhile, heat the olive oil in a large saute pan over medium heat. Add the diced onion and cook until soft; about 3 minutes. Stir in red pepper flakes and garlic and cook for 1 minutes before adding the tomatoes and a pinch of salt and pepper. Cook until the tomatoes just begin to blister, about 2 minutes. Add a ladle full of the pasta water (about ¾-1 cup) and the chopped basil to the tomatoes.

Add the pasta to the saute pan and bring to a boil. The liquid will reduce as the pasta finishes to form a sauce; 3-4 minutes. Stir in 1/3 cup fresh grated Parmesan.

Season with salt and garnish with fresh grated Parmesan cheese.