While the onions are cooking, peel the squash, cut in half, and remove the seeds. Cut the squash into chunks. Peel, quarter and core the apples. Cut the apples into chunks. Add the squash, apples, salt, pepper and a 1 1/2 cups of water to the pot. Bring to a boil, then cover, reduce the heat to low and cook for 30 to 40 minutes, until the squash and apples are tender. Process the soup through a food mill or puree it coarsely in a bowl of a food processor fitted with a steel blade. If you own an immersion blender, this is a good recipe to use it.