Preheat oven to 400 degrees.
In a medium stockpot cook your bacon until crispy, remove bacon from pot.
Place the butternut squash and pepper onto a sheet pan a drizzle with half of the bacon fat. Place into oven and bake until squash is tender, about 25-30 minutes.
Saute the onion and garlic in the bacon fat left in the pot until the onions are translucent.
Add in the squash, peppers, salt, pepper and thyme.
Cook for an extra five minutes.
Stir in the stock, blend with an immersion blender until smooth.
Bring soup to a boil than let it simmer for 10 to 15 minutes.
Top with a dollop of yogurt, bacon and scallions.