Melt butter in a large pot over medium-high heat. Saute butternut squash, leeks, carrots, and celery in hot butter until vegetables are softened, 10 to 12 minutes.
Stir apples, thyme, and sage into the squash mixture; pour in chicken stock and cider. Bring mixture to a simmer, reduce heat to low, cover pot with a lid, and cook until vegetables and apples are tender, about 30 minutes. Remove soup from heat and cool slightly, about 10 minutes.
Pour soup into a blender no more than half full. Cover and hold lid down; pulse a few times before leaving on to blend. Puree in batches until smooth. Return mixture to pot and season with salt to taste. Garnish individual servings with crumbled bacon.
You can also use a food processor or immersion blender to puree the soup.