Heat the olive oil in a large pan over medium heat. Once the oil is shimmering, add the chopped yellow onion and cook, stirring occasionally, until the onion is softened, about 3 minutes. Add the minced garlic and continue to cook until fragrant, about 30 seconds. This step sets a fragrant base for your sauce.
Add the ground beef to the pan with the cooked onions and garlic. Sprinkle in the fine sea salt, cracked black pepper, and red pepper flakes. Cook, crumbling the beef with a spoon, until the meat is nicely browned and cooked through. If there is excess grease in the pan, drain it off as needed.
Add the tomato paste and granulated sugar to the browned meat. Cook, stirring almost constantly, until the tomato paste darkens in color and becomes caramelized, about 1-2 minutes. Drizzle in the dry red wine, scraping up any browned bits from the bottom of the pan. Let the wine cook until it reduces by about half and the harsh smell of alcohol is mostly gone, which should take 3-5 minutes. I like to take a moment here and really scrape the pan well—a bit of fond makes the sauce extra delicious.
Pour in the water and add the canned whole peeled tomatoes. Break or crush the tomatoes with your spoon so they integrate well into the sauce. Sprinkle in the basil, parsley, oregano, and toss in the bay leaf. Stir everything until well combined and ensure the bay leaf is submerged. Simmer the sauce, partially covered (offset lid), for at least 30 minutes, stirring occasionally to prevent sticking or burning.
While the sauce is simmering, bring a large pot of salted water to a boil. Add the spaghetti (or pasta of choice) and cook according to the package instructions until al dente. If you plan to mix the pasta and sauce together, reserve about 1/4 cup of the pasta cooking water before draining. Add the cooked pasta (from this step) to the simmered meat sauce (from Step 4), along with a splash of the reserved pasta water. Stir well and let simmer for a few minutes until the sauce clings to the noodles. Personally, I always use the pasta water trick—it's a great way to help the sauce stick to the pasta for a restaurant-style finish!
Serve the meat sauce over the portioned pasta or pre-mixed sauced noodles. Top with parmesan cheese if desired. Enjoy your delicious homemade pasta!