Preheat your oven to 425°F. Toss cubed butternut squash with 2 tablespoons olive oil, salt, and pepper on a sheet pan. Roast for 20 minutes until edges are golden and fork-tender.

While squash roasts, bring a large pot of salted water to boil. Add pasta and cook according to package directions until al dente. Reserve one cup of pasta water before draining.

Heat remaining 1 tablespoon olive oil in a large skillet over medium heat. Sauté diced onion for 3 minutes, then add minced garlic and thyme. Cook until fragrant, about 1 minute more.

Add roasted butternut squash and vegetable broth to the skillet. Simmer gently for 5 minutes to blend flavors. Stir in fresh sage carefully to preserve its delicate texture.

Pour in heavy cream and butter, stirring until butter melts completely. Add nutmeg and taste for seasoning adjustments. The roasted butternut pasta sauce should coat the back of a spoon smoothly.

Add cooked pasta directly to the cream sauce, tossing gently to coat every piece. If the mixture seems thick, add reserved pasta water one tablespoon at a time until reaching desired consistency.

Remove from heat and stir in grated parmesan cheese until fully incorporated. Top with additional fresh sage and cracked pepper before serving immediately.