Preheat the oven to 425 F. Line a large baking sheet with parchment paper and set aside.
While the oven is preheating, prepare the ingredients that will be roasted.
Peel the butternut squash and scoop out the seeds. Dice it into about 1-inch cubes. Chop shallots, garlic cloves, celery, carrots and apple. Keep in mind that after roasting we will be using an immersion blender to puree these ingredients so don’t spend too much time making sure everything is the correct size and shape.
Layer the butternut squash, carrots, celery, shallot, garlic cloves, and apple on the lined baking sheet. Drizzle with 3 tbsp. of olive oil and toss lightly. Top with thyme sprigs and place in the oven. Roast for about 30 minutes or until the squash and carrots are fork tender. Flip the vegetables using a spatula at least once throughout the roasting process.
While the vegetables are roasting, mince the sage leaves and peel and grate the ginger. This would also be a good time to cook the bacon and chop the chives for serving.
When the vegetables are done roasting remove the baking sheet from the oven. The leaves should have fallen off from the thyme sprigs and you can discard the woody stems. Transfer the vegetables to a large stock pot or Dutch oven and place it on the stovetop.
Add the broth, grated ginger, minced sage, salt, and pepper to the stock pot and stir. Bring the broth to a boil, then reduce heat and allow it to simmer for about 10 minutes.
Remove the soup from the heat. Carefully use an immersion blender to blend the soup until the vegetables are fully pureed and no chunks remain. This can also be done by using a high powdered hot/cold blender. You will need to blend in batches if using this method. It is helpful to let the soup cool partially before transferring it to the blender pitcher.
Once pureed, stir in your milk of choice until the soup is a uniform creamy orange color.
Serve the soup hot topped with chopped, cooked bacon, chopped chives, and a swirl of cream.
Leftovers can be stored in an airtight container in the fridge for 3-4 days or in the freezer for up to 2 months.