Heat olive oil in a large skillet over medium heat. Add chopped onion and cook for about 10 minutes until soft and translucent.
Stir in minced garlic and crushed red pepper flakes; cook for 3 minutes until fragrant.
Pour in pureed San Marzano tomatoes and sprinkle with kosher salt. Stir and allow to simmer for about 20 minutes.
Fold in chopped fresh basil just before the sauce finishes cooking.
Meanwhile, bring a large pot of salted water to a boil. Cook spaghetti according to package instructions until al dente, reserving half a cup of pasta water before draining.
Return drained spaghetti to the pot. Pour the tomato sauce over the pasta and add reserved pasta water. Toss to coat.
Add butter pieces and Parmesan cheese, tossing until melted and combined.
Serve immediately, garnished with extra basil and Parmesan cheese.
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Notes
Store leftovers in airtight containers in the refrigerator for up to 3 days. Reheat gently on the stove.