Preheat the oven to 375 degrees F.
Halve the pumpkin from top to bottom and place it, cut side down, on an oiled baking sheet. Bake until the pumpkin can be easily skewered, 45 to 60 minutes. Cool for about 20 minutes.
With a spoon, remove the seeds and discard. Scrape the pulp and reserve. Discard the skin. Melt butter in a soup pot over medium heat. Add the bacon and onions and cook, stirring occasionally, until the onions are soft and the bacon is just turning golden, about 7 minutes. Add the pumpkin and stock and simmer until the pumpkin falls apart, about 30 minutes. Let cool for about 20 minutes.
In batches, puree the soup in a blender on high speed, 3 minutes per batch, until very smooth. Strain through a fine mesh into a clean soup pot and add the cream, orange juice and nutmeg.
Season, to taste, with salt and pepper. If the soup is too thick, correct the consistency with additional water or stock. Chop 1 tablespoon chipotle pepper. Whip 1 cup cream to soft peak. Stir peppers into cream. Ladle the hot soup into bowls. Spoon dollop of chipotle cream into soup.
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