Place the onion, carrot, and celery pieces in the bowl of your food processor. Turn on and run for a minute or so until the vegetables are very finely minced, almost like a paste.
Drizzle the olive oil into a Dutch oven or large pot and bring over medium heat. When the oil is hot, add the finely minced vegetables from step one and stir to coat with the oil. Spread across the bottom of the pot and cook, stirring occasionally, for 3-4 minutes until softened.
Add the ground beef, salt, and black pepper to the pot and use a cooking spoon or spatula to stir in and break up the meat. Cook, breaking the meat into crumbles, for about 5 minutes or until browned. Add the garlic, oregano, and red pepper flakes and stir into the meat and vegetables. Cook for an additional minute.
Pour in the wine and stir together, scraping up any stuck-on bits from the pot. Simmer the mixture for 3 minutes over medium until the wine is mostly absorbed.
Add the can of crushed tomatoes, the tomato paste, balsamic vinegar, and Better Than Bouillon beef base. Stir until combined and allow to come to a boil. Reduce the burner heat to low and allow to simmer for 10 minutes, stirring occasionally.
Add the nutmeg, half and half, and water and stir until well combined. Continue to simmer uncovered over low heat for another 10 minutes, stirring occasionally.