Heat oil in a Dutch oven over medium heat. Add onion, garlic, ginger and jalapeño and sauté 5 minutes or until onion is softened. Add squash, sprinkle with sugar, and sauté 5 minutes or until crisp-tender.
Add apples, chili powder, salt and thyme and stir to coat. Add stock and 1 1/2 cups water and bring to boil. Reduce heat and simmer, partially covered, 30 minutes or until squash is tender.
Working in batches, transfer to a blender or food processor, cover, and puree until smooth. Return squash and apple soup to pan and cook until heated through.