In a large stockpot or Dutch oven over medium-high heat, add the olive oil. Next, add the apples, squash, garlic and onions and saute until the vegetables begin to sweat and soften, about 5 minutes. Add the sage, ground nutmeg and salt and pepper to taste and continue to cook another 2 minutes. Add the stock, making sure that it covers the squash; if necessary, add a little water. Bring the soup to a boil and then reduce the heat to medium low. Simmer until the squash is very tender, about 30 minutes.
Using an immersion blender, blend the soup until smooth. Stir in the heavy cream, Parmesan and butter. Serve immediately.