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Heat one tablespoon of olive oil in a skillet over medium/high heat. Liberally season the short ribs with salt and pepper and sear on all sides until golden brown, about 4 minutes per side.
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Add short ribs, garlic, onion, crushed tomatoes, tomato sauce, diced tomatoes, tomato paste, red wine, oregano, thyme, basil, bay leaf, and red pepper flakes to crock pot. Cook for 5-6 hours on high or 8-10 on low.
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Once sauce is finished, remove short ribs, discard bones, and shred the beef. Add the shredded beef back into crockpot and cook for another 30 minutes to an hour.
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When ready to serve, preheat the oven to 400℉. Line a large rimmed baking sheet with parchment and add butternut squash noodles. Drizzle with remaining tablespoon of olive oil and season with salt and pepper. Toss to coat.
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Roast for 10 minutes until just "al dente". Serve with the sauce, fresh parm, and basil.