Heat olive oil in a large skillet over medium-high heat and add the diced onion. Cook for 3-4 minutes until softened, then add minced garlic and cook another 30 seconds until fragrant. This builds the flavor foundation for your entire dish.
Add the cubed butternut squash to the skillet and stir to coat with oil. Cook for 8-10 minutes, stirring occasionally, until the squash is completely tender and easily pierced with a fork. The cubes will begin breaking down naturally into the sauce.
Pour in the vegetable broth and simmer for 2 minutes to allow flavors to meld. Remove from heat and carefully blend the mixture using an immersion blender until completely smooth and creamy. Work in batches if using a standard blender, being careful with hot liquid.
While the squash simmers, bring a large pot of salted water to a rolling boil. Add your pasta and cook according to package directions, then drain and reserve 1 cup of pasta water. This starchy water helps create the silkiest texture in your creamy silky butternut squash pasta.
Return the blended squash mixture to the skillet over medium heat and stir in butter, heavy cream, nutmeg, and salt and pepper. Simmer for 2-3 minutes until the sauce reaches your desired consistency, adding pasta water a splash at a time if needed. The sauce should coat the back of a spoon beautifully.
Add the cooked pasta directly to the sauce and toss gently to coat every piece. Stir in fresh sage and half the parmesan cheese, reserving the rest for garnish. Taste and adjust seasoning—remember that parmesan adds saltiness, so go easy on additional salt.
Divide among serving bowls and top with remaining parmesan, toasted pine nuts, and a pinch of red pepper flakes for heat contrast. The red pepper flakes brighten the creamy pasta while the pine nuts add sophisticated crunch.