Bring a large pot of salted water to a rolling boil, adding enough salt to make it taste like the sea. Once boiling, add the spaghetti and stir immediately to prevent sticking. Cook until al dente, about 8-10 minutes, then drain and set aside.
While the pasta cooks, heat the olive oil in a sauté pan over medium heat. Add the crushed garlic and cook gently until fragrant, about 30 seconds, until it releases a sweet aroma. Add the finely chopped basil stems and stir quickly, cooking for another 15 seconds until aromatic.
Add the diced fresh tomatoes or canned San Marzanos to the pan. Stir and cook at medium heat for 5-7 minutes, allowing the tomatoes to break down and the sauce to thicken slightly. Season with salt, pepper, and chili flakes if using, adjusting to taste.
Once the sauce is fragrant and slightly thickened, add the drained spaghetti directly into the pan. Toss well with tongs or a wooden spoon, allowing the pasta to soak up the flavors. If the sauce seems thick, add a splash of reserved pasta water to loosen it up and help it cling to the noodles.
Taste the dish and adjust seasoning as needed, adding more salt or pepper. Turn off the heat and stir in the fresh basil leaves, letting their aroma bloom for about 30 seconds.
Serve the pasta hot, garnished with extra basil leaves if desired. Drizzle with a little more olive oil for richness and enjoy the vibrant, herbaceous flavors.