In a large, wide pot, heat the olive oil over medium-low heat and add the peeled garlic. Cook, stirring occasionally, until the garlic turns golden brown on all sides, which should take about 8 to 10 minutes. If the garlic starts to burn, reduce the heat.

While the garlic is cooking, break the whole tomatoes into smaller pieces using a paring knife or kitchen shears.

When the garlic is nearly done, add the red pepper flakes and cook for about 30 seconds until they are toasted and fragrant.

Stir in the tomatoes, bay leaves, kosher salt, oregano, and freshly ground pepper. Use a wooden spoon to break up the tomatoes and mix everything together until well combined.

Increase the heat slightly and let the sauce simmer gently, stirring occasionally, for at least 2 hours, or up to 3 hours, until it thickens and the flavors concentrate.

In a medium bowl, combine the torn Italian bread with the milk and let it sit for about 5 minutes until moistened. Afterward, squeeze the bread to remove excess milk and discard the milk. Tear the bread into smaller, pea-sized pieces and return it to the bowl.

In a large bowl, mix together the ground beef, ground pork, ground veal, beaten eggs, finely chopped garlic, 1 cup of grated Parmesan, ½ cup of chopped parsley, 1 teaspoon of kosher salt, oregano, freshly ground black pepper, ground fennel seeds, and red pepper flakes. Gently incorporate the moistened bread into the mixture using your hands, being careful not to overmix.

Fill a small bowl with cool water. Moisten your hands and roll the meat mixture into golf-ball-sized meatballs, occasionally wetting your hands as needed. Place the meatballs on a rimmed baking sheet; you should have about 24 meatballs. Chill them until the sauce is ready.

After the sauce has simmered for 2 to 3 hours, remove the bay leaves and stir in the basil. Use an immersion blender to purée the sauce until it is slightly chunky but not completely smooth. Reserve 1 ½ cups of the sauce and keep the remaining sauce warm in the pot over very low heat.

In a large skillet, heat the remaining olive oil over medium-high heat. Once hot, add the meatballs in batches, making sure not to crowd the pan. Brown the meatballs on all sides, turning them frequently, which should take about 5 minutes per batch. Transfer the browned meatballs back to the baking sheet.

Once all the meatballs are browned, add them to the pot with the tomato sauce. If your pot is too small, you can divide the sauce and meatballs between two pots. Increase the heat to medium-low, cover, and let them simmer until the meatballs are cooked through, about 10 to 15 minutes.

Meanwhile, cook the spaghetti in a large pot of boiling salted water, stirring occasionally, until it is al dente. Drain the spaghetti, reserving 1 cup of the pasta cooking liquid, and return the pasta to the pot over medium-low heat.

Pour the reserved 1 ½ cups of sauce over the spaghetti and toss to coat. Add the reserved pasta cooking liquid, ¼ cup at a time, as needed to loosen the sauce and ensure it coats the pasta evenly.

Serve the pasta on plates, topped with the meatballs and the remaining sauce. Finish by sprinkling the remaining ¼ cup of grated Parmesan and ¼ cup of chopped parsley on top.

The sauce can be made ahead, cooled, and stored in the refrigerator for up to 5 days or frozen for up to 3 months. The meatballs can be shaped and refrigerated a day in advance, and they can also be cooked in the sauce, cooled, and stored in the refrigerator for up to 5 days or frozen for up to 3 months.