Bring a large pot of salted water to a boil. Add the penne pasta and cook according to package instructions until al dente. Reserve about a cup of pasta water before draining the pasta in a colander. Set aside.
Heat the olive oil in a large skillet over medium heat. Add the chopped onion and cook until soft and translucent, about 5 minutes. Stir in the minced garlic and red pepper flakes, cooking for another 1-2 minutes until fragrant.
Pour in the fire-roasted crushed tomatoes and stir to combine. Add the sugar along with salt and pepper to taste. Reduce the heat to low and let the sauce simmer gently for 15-20 minutes, allowing the flavors to meld and the sauce to thicken slightly.
Add the drained penne pasta directly into the skillet with the sauce. Toss well to coat every piece of pasta. If the sauce feels too thick, add a splash of the reserved pasta water to loosen it up and help it cling to the noodles.
Serve hot with a generous sprinkle of freshly grated Parmesan cheese and torn fresh basil leaves for a burst of color and herbaceous brightness.
