Prepare your pasta according to package directions. Drain and set aside.
While pasta is cooking, heat a large sauce pan over medium heat and add butter, when melted add onions. Whisking occasionally until butter browns and small brown bits appear in the pan. Immediately whisk in flour, salt, pepper and cook 1-2 minutes. Whisk in warmed milk, when flour mixture has incorporated into milk continue to cook and stir until starts to boil, then add cottage cheese, squash, nutmeg and sage, mixing until well combined. The amount of milk will depend on your squash, if it's on the drier side you'll need to add all the milk . At this point taste to see if more seasoning is needed. I tend to add more salt. Stir in 1 cup of Fontina cheese.