Combine uncooked spaghetti, tomatoes, onion, garlic, torn basil (reserving the chiffonade leaves for garnish), 2 Tbsp. olive oil, 2 tsp. salt, half the red pepper flakes (reserving remaining for garnish, if desired), and 4 ½ cups of water in large pot. Bring to a boil over high heat uncovered. Boil mixture, stirring and turning pasta frequently with tongs, until pasta is al dente and water has nearly evaporated, about 9 minutes.