01 - Bring a large pot of salted water to a rolling boil over high heat.
02 - Add penne pasta and cook according to package directions until al dente, approximately 8-10 minutes. Reserve 1/2 cup of starchy pasta water before draining thoroughly in a colander.
03 - While pasta cooks, heat olive oil in a large skillet over medium heat. Add chopped garlic and diced onion, sautéing for 2-3 minutes until fragrant and translucent, taking care not to brown the garlic.
04 - Pour in diced tomatoes with their juices and stir in tomato paste. Add dried oregano, chili flakes, salt, and black pepper. Simmer uncovered for 5-7 minutes, stirring occasionally, until sauce slightly thickens and flavors meld.
05 - Transfer drained pasta directly into the skillet with the tomato sauce. Toss vigorously with tongs or a wooden spoon to coat every piece, adding reserved pasta water a tablespoon at a time if sauce appears too thick.
06 - Remove from heat and fold in chopped fresh basil and grated Parmesan cheese. Let rest for 1 minute to allow cheese to melt into the sauce. Serve immediately in warmed bowls, offering additional Parmesan and whole basil leaves at the table.