Sauté Aromatics: Heat 2 tablespoons of olive oil in a large pot over medium heat. Add the diced shallots and cook until they become soft and translucent, about 4 to 5 minutes. Stir in the minced garlic and bay leaves, then season with ½ teaspoon of salt, ½ teaspoon of black pepper, and the crushed red pepper flakes. Let the flavors meld together, cooking for about 2 minutes.
Blend Tomatoes: While the aromatics cook, blend the fresh tomatoes until smooth, working in batches if necessary. Pour the blended tomatoes into the pot, followed by the chopped thyme. Reduce heat to a gentle simmer.
Prepare the Meat: In a separate skillet over medium-high heat, add the remaining olive oil along with the ground beef. Sprinkle in the garlic powder, dried oregano, and another ½ teaspoon of salt and black pepper. Cook while stirring, breaking up the meat into crumbles, until browned, about 5 to 7 minutes. Drain any excess grease, then return the cooked beef to the pan. Stir in the Pecorino Romano cheese and cook for another minute.
Combine Ingredients: Transfer the beef mixture to the pot with the tomato sauce. Pour in the beef stock and stir in the tomato paste. Scrape up any bits from the bottom of the pan and mix well. Bring everything to a boil, then reduce the heat to low and let it simmer uncovered for about 10 minutes.
Final Seasoning: Stir in the remaining salt and black pepper, followed by the sugar and soy sauce. Let the sauce cook on low heat for an additional hour, stirring occasionally to let the flavors fully develop.
Cook the Pasta: While the sauce simmers, bring a large pot of salted water to a boil. Cook the spaghetti according to package instructions until al dente. Before draining, reserve about 3 tablespoons of the pasta water, then drain the rest.
Finish and Serve: Stir the reserved pasta water into the sauce to help bind it together. Remove the bay leaves, then toss the spaghetti into the sauce, coating each strand with the rich, meaty mixture. Serve hot and enjoy your soul-satisfying spaghetti!