Cook the pasta 1 minute shy of al dente and set aside, reserving some of the pasta water.
Add the oil to a skillet with enough room to fit the sauce and the pasta. Cook on medium for a couple of minutes, then add some basil stems, the garlic, and a pinch of red pepper flakes if using. Allow this to cook gently, making sure to not burn anything. Cook about 3-5 minutes.
Add the tomatoes and a pinch of salt. Stir to coat the tomatoes in the oil, then lower the heat to low and cover. Let cook for about 10-15 minutes, or until the tomatoes are soft enough to smoosh with the back of a wooden spoon.
Smoosh the tomatoes, then let simmer for another couple of minutes. Remove the basil stems and garlic, then add in plenty of fresh basil leaves.
Add the cooked spaghetti and stir to coat in the sauce, adding a touch of the reserved pasta water if needed.
Add the spaghetti to a plate, making sure to spoon the leftover sauce on top. Add a good grating of freshly grated Locatelli or Parm, more fresh basil, and red pepper flakes if using.