Cook bacon in large soup pot until crisp. Remove the bacon drain on paper towels. Pour all the drippings into a heat proof container. Return 2 tablespoons of the drippings to the soup pot and add the onion. Sweat for 3 or 4 minutes, until the onions begin to soften.
Raise the heat to medium high and add the squash and apples. Cook, stirring occasionally until everything is slightly browned. Add the apple juice and stir to de-glaze the pan. Add the stock and bring to a boil. Reduce the heat to simmer, add the sage and cook, covered 30 minutes or until the squash is soft. remove from heat and puree with an immersion blender.
While soup is simmering, heat a tablespoon of the bacon drippings in a small fry pan. Add the shallots and cook until carmelized, 15 minutes or so. Set aside for garnishing the soup.
Return the pot of soup to the stove and simmer over low heat for a few minutes. Add the cream and heat gently until everything is steamy. Add salt and pepper to taste. If soup is too thick, add a little more stock or cider. If Soup is too thin, add 2-3 tablespoons of potato flakes. Heat until any additions come up to temperature.
Ladle soup into bowls. Top each bowl with some of the bacon and shallots and sprinkle with the pepitas.