Preheat your oven to 375 degrees. In a large, deep stockpot or Dutch oven, heat the olive oil over low. Add the onions and cook until very tender, about 15 to 20 minutes, stirring occasionally.While the onions cook, cut and peel the squash and apples. Add them to the pot, then add 2 cups of the stock. Bring the pot to a boil, reduce the heat to low, then cover, and cook until the squash and apples are very soft, about 20 to 30 minutes depending upon how larger you cut your squash and apple pieces (smaller pieces will cook more quickly).Meanwhile, prepare the croutons. Place the bread cubes on a large baking sheet. Drizzle with olive oil, sprinkle with sage and salt, then toss to coat. Spread the cubes in a single layer, then bake until lightly crisp and brown, 10 to 12 minutes, tossing once halfway through. Sprinkle with Parmesan cheese, toss to coat, then set aside until ready to serve.Once the apples and squash in the soup pot are tender, puree the soup with an immersion blender or carefully transfer it to a food processor fitted with a steel blade to puree in batches. Return soup to the pot once complete. Add 1 cup of the remaining chicken stock, then stir, adding a bit more stock as needed to reach your desired consistency (the soup will thicken somewhat when stored). Leave the texture fairly thick and rich. Stir in the salt, nutmeg, black pepper, and cayenne. Taste and add a bit more salt and pepper as desired. Serve hot, topped with sage croutons.