Pour 1/4 cup of water into a large saucepan and place saucepan over medium heat. Boil the onion for 3 minutes or until tender, taking care to avoid letting all of the water evaporate.
Add the remaining water and next four ingredients (pumpkin through nutmeg) to the saucepan. When the water begins to boil, reduce the heat. Allow the mixture to simmer for 5 minutes, then add the milk and continue to cook until the soup becomes hot.
Ladle equal portions of the soup into four individual bowls. Top each portion with black pepper and green onions if desired. Serve immediately.