Preheat the oven to 400.
Cut off the top stem of the squash. Then cut lengthwise in half and place in a glass baking dish, facing down. Add about 1/4" of water to the baking dish. Cover with foil. Bake in the preheated oven for 45 minutes, or until completely soft. Check to make sure the squash is tender in the thickest portion by poking with a fork. Cooking time may vary depending on thickness of the squash.
Meanwhile, add the olive oil to a large saucepan and saute the apples, pear and onion for about 5 minutes. Then pour in the chicken broth and milk/cream and bring to bubbling. Add the seasonings and spices. Reduce heat to low and keep simmering until squash is ready. (If longer than 10 minutes, cover tightly while it simmers so too much water doesn't boil off.)
When the squash is cooked through, carefully flip it over (you will need an oven mitt!) and scoop out the seeds. Then scoop the soft flesh out and add to the bubbling soup.
Transfer to a blender and puree.
Serve with a nutmeg garnish. Season to taste.