Step 1

In a large skillet, heat the olive oil over medium heat. Add the onions and cook, stirring occasionally, until softened, 8 to 10 minutes. Add the red pepper flakes and garlic and cook a little longer. Add the tomatoes with the juices from the can and the sugar and stir to combine. Cook, stirring from time to time and crushing the tomatoes with the back of a wooden spoon as they soften, until the sauce is thickened slightly, an additional 15 to 20 minutes. Season with salt.

Step 2

Meanwhile, bring 4 quarts of water to a rolling boil in a large pot. Add a generous handful of salt. Bring the water back up to a boil. Add the penne, stirring the pasta with a slotted spoon to make sure it does not clump or stick to the bottom of the pot as it cooks. Cook until just al dente according to the package directions.

Step 3

Reserve 1/2 cup of the pasta-cooking liquid in case you need to thin out the sauce, then drain the pasta in a large colander and add to the sauce. (Alternatively, use a spider or slotted spoon to transfer the pasta directly into the sauce.) Toss to coat with the sauce. Remove from the heat and allow the pasta to “rest” for a few minutes. If the sauce is too thin, gently warm and reduce over low heat for an additional 1 to 2 minutes. If too thick, simply thin it out with some of the reserved pasta-cooking liquid. Stir in some of the Parmesan and then serve topped with remaining Parmesan.