1. Preheat oven to 350 degrees Fahrenheit.
2. Place whole squash on a rimmed baking sheet and roast until tender and soft, about one hour and 15 minutes. Cool.
3. While squash cools, heat oil in a large pot over medium heat. Add onion, garlic and apple, and cook, covered, until onion is translucent and apple is tender, about five minutes. Add nutmeg, cinnamon, cardamom, cumin, ginger, and cloves and cook, stirring constantly, until fragrant, about one minute.
4. Halve cooked squash lengthwise, then scrape and discard seeds. Scoop out flesh and add to onion-apple mixture. Add broth, salt, and pepper and cook until heated through.
5. With an immersion blender or a food processor, puree soup until smooth.
6. Ladle warm soup into bowls and serve with a dollop of sour cream, candied pecans, thinly sliced apples, and pomegranate seeds.
