Preheat your oven to 400 degrees. Line a baking sheet with aluminum foil.
Halve your acorn squash and scrape out the seeds.
Place the acorn squash halves skin side down on the baking sheet and rub with olive oil. Lightly salt then place in the oven for 40 minutes (or until soft under the poke of a fork).
After 20 minutes of the squash being in the oven, place the chopped onions and garlic on a separate aluminum foil-lined baking sheet. Roll in olive oil, sea salt, and cracked pepper. Place in the oven for the remaining time left for the acorn squash (about 20 minutes).
In a separate bowl, combine the greek yogurt, lemon juice, sea salt, and sage together. Set aside until serving time.
When the squash and onions/garlic are finished in the oven, take them out and set aside. Wait about 15 minutes or until the squash is cool enough to lightly handle.
In a large soup pot, bring the chicken stock to a low simmer.
Use a large spoon and start spooning the flesh away from the skin of the squash. Drop the squash flesh and roasted onions/garlic into the soup pot. Add the ginger, nutmeg, and vanilla.
Bring the mixture up to a low simmer then either transfer to your blender or use your immersion blender directly in the pot.
Blend until the soup is smooth. You may add cracked pepper and more sea salt at this time if your taste desires.
Pour a few ladles into your favorite bowl and top with a healthy dollop (about 2 T) of the sour cream. I recommend scraping a bit with each spoonful of soup.