Prepare pasta according to package instructions, drain and set aside.
Heat butter in skillet on low to medium heat and add onions. Saute for 15-20 minutes until fragrant and brown.
While onions are cooking, remove the skin and seeds from squash and cut flesh into cubes (or purchase already peeled and cubed butternut squash). Bring broth to a boil in a large pot and add squash. Cook for 7 minutes, stirring frequently.
Drain squash, reserving 1/2 cup of broth. Add squash, reserved broth, milk, sea salt and cooked onions to a blender and process until smooth.
Pour sauce over pasta, stirring to coat. This recipe makes a bit more sauce than you will need. No worries…store in an airtight container and refrigerate for later in the week.
Stir in cheese and mix until melted throughout. Season with salt and pepper to taste!