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Fill a large pot with water, add a generous pinch of salt, and bring to a rolling boil over high heat.
Once boiling, add 1 pound penne pasta, stir occasionally to prevent sticking, and cook until al dente (about 10–12 minutes).
Before draining, scoop out 1 cup of pasta water and set aside. Drain the pasta and set aside.
Meanwhile, heat 2 tablespoons olive oil in a large skillet or Dutch oven over medium heat.
Add 1 small yellow onion, finely chopped, and cook for 5–7 minutes until softened and translucent.
Add 3 cloves garlic, minced, and cook for 1 minute more until fragrant.
Pour in 28 ounces crushed tomatoes, then stir in 1 teaspoon dried oregano, 0.5 teaspoon salt, and 0.25 teaspoon black pepper. Bring to a gentle simmer.
Reduce heat to low, cover, and simmer the sauce for 15 minutes, stirring occasionally (up to 30 minutes for deeper flavor).
Stir in 0.25 cup fresh basil leaves, roughly chopped.
Add the cooked penne pasta to the sauce, toss to coat, and add reserved pasta water as needed to reach desired consistency.
Serve immediately, topped with freshly grated Parmesan cheese.