While the onions are cooking, peel the squash, cut it in half and remove the seeds. Cut the squash into chunks. Peel, quarter and core the apples, then cut them into chunks as well. Add the squash, apples, salt, pepper and 1½ cups of water to the pot. Bring to a boil, then cover, reduce the heat to low, and simmer for 30 to 40 minutes, until the squash and apples are tender. Purée the soup using a food mill, a food processor fitted with a steel blade, or an immersion blender for easy blending right in the pot.