In a large pot, cook the bacon on low/medium heat, stirring occasionally, until crisp and golden, 8 to 10 minutes. Use a slotted spoon to transfer the bacon to a plate lined with paper towels. Do not discard bacon fat!
Increase heat to medium high. Add the squash to the pot with the bacon fat and cook until lightly browned, 4 to 6 minutes (if you stir it too often, it wont brown, so only stir from time to time). Stir in the apple, sage, salt, and pepper and cook for about 4 minutes. Add broth, scraping up any browned bits in the pot with a wooden spoon. Bring to a boil, reduce the heat to maintain a light simmer, and cook until the squash and apples are very soft, about 7 minutes. Remove from heat and let cool somewhat.
Add about half the bacon to the soup and purée. Taste and add more salt and pepper if needed. Reheat the soup and garnish each serving with the remaining bacon