In a large pot or dutch oven heat up the olive oil on medium-low heat. Add the chopped onions stirring them around to coat them with the oil. Lower the heat to low (2-3 on the stovetop). Let the onions cook for 40-50 minutes on low, occasional stirring. The onions should soften and smell great, but you are not trying to brown them. Add the garlic and cook on low for another 10 minutes.

Next, add all the other ingredients (diced tomatoes, tomato paste, salt, fresh ground pepper, red pepper flakes oregano, basil, and water). Bring the sauce up to a boil on medium-high and then lower it to medium-low (3-4 on the stovetop) to simmer for ~2 hours stirring occasionally.

If the sauce becomes thicker than you desire add a ½-1 cup of water a cook for another 20 minutes.