Preheat oven to 450°.
In a large bowl, toss squash, garlic, and thyme together with oil to coat. Transfer to a 9 x 12 inch pyrex baking dish. Sprinkle generously with salt and fresh ground pepper, and bake for about 35 minutes, stirring occasionally, until squash is soft and just turning brown.
While the squash bakes, cook the bacon in a stovetop skillet until just crispy. Remove bacon and toss leeks into skillet cooking in bacon fat until the leeks are tender and translucent, about 5 minutes.
When squash is done, remove from oven and transfer into a large soup pot along with leeks and pan drippings.
Pour stock into pot to cover squash/leek mixture about a half inch over. Add more stock if needed for this.
Bring to a boil then turn down heat and let simmer, partially covered, for about 3o minutes.
Remove soup from heat and purée with immersion blender, or in batches in a regular blender, until smooth. Add milk and blend another minute or two until desired creamy consistency is reached.
Crumble or chop the cooked bacon and stir into the creamed soup.
Reheat if necessary and serve.