Pre-heat oven to 400 degrees.
Line a baking sheet with foil and place diced butternut squash, chopped onions, and garlic in a single layer. Lightly drizzle with olive oil and sprinkle with salt and pepper. Toss to combine.
Bake for 25-30 minutes, until squash is tender.
Put squash, onion, and garlic in a medium-sized pot or dutch oven over medium heat, along with vegetable broth, chipotle peppers, and nutmeg. Stir to combine and cook for about 2 minutes.
Puree soup in pot with an immersion blender or pour into a blender to puree until completely smooth.
Pour back into pot and bring to a boil before lowering heat to a simmer for about 5 minutes.
Turn heat off and mix in coconut milk and lime juice.
To serve, pour soup into bowls and swirl additional coconut milk on top. Top with diced avocado, chopped basil or cilantro, and grilled cheese croutons.