Bring a large pot of salted water to rolling boil and add pasta, cooking according to package directions. Reserve 1 cup pasta water before draining, which will help adjust your sauce consistency later.
While pasta cooks, heat olive oil and butter in a large skillet over medium-high heat. Add diced onion and sauté for 3 minutes until softened, then add minced garlic and cook 1 minute more until fragrant.
Add cubed butternut squash to the skillet along with vegetable broth and bring to simmer. Cook for 8-10 minutes until squash is completely tender and easily pierced with a fork.
Pour in heavy cream, add nutmeg, salt, pepper, and red pepper flakes, stirring constantly. Let this butternut squash pasta sauce simmer 2-3 minutes to meld flavors beautifully together.
Stir in grated parmesan cheese and fresh sage, tasting and adjusting seasonings as needed for your preference. Add reserved pasta water gradually to reach desired sauce consistency.
Add cooked pasta to the skillet and toss gently until every strand is coated in creamy sauce. If the mixture seems too thick, add more pasta water one tablespoon at a time.