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.