Caramelize the onions: Heat the butter in a large skillet over medium-low heat. Cut the onion into thin slices and add to the melted butter in the pan. Keeping the heat on medium-low, cook the onions until they are caramelized and deep golden brown, about 20-30 minutes. You can add a splash of white wine as they’re cooking to get a little extra sweetness.
Make the sauce: Puree the garlic, pumpkin, chicken broth, milk, olive oil, salt, sage, nutmeg, and pepper in a blender until smooth. Add to the caramelized onions in the pan and cook until heated through.
Prep pasta and chicken: Cook the pasta according to package directions, stopping a little early so they are still firm enough to hold their shape in the oven. Drain and set aside. Meanwhile, bring a pot of water to boil and add the chicken, cooking for 10-15 minutes or until the chicken is no longer pink. Remove from the water; when cool enough to handle, shred the chicken.
Assemble and bake: Preheat the oven to 350 degrees. Toss the cooked pasta, chicken, and bacon with the pumpkin sauce and 1/2 cup Mozzarella cheese. Transfer to a greased 9×13 baking dish, top with remaining cheese and cover with greased foil to prevent sticking. Bake for 15-20 minutes or until the cheese is melted and the sauce is bubbling. Sprinkle with fresh parsley and let stand a few minutes before serving.