Preheat the oven to 350°F. Peel the squash and apples. Once peeled, cut the squash in half, remove the seeds and dice it into one-inch cubes. Next, thinly slice the apples.
Cover with foil and bake casserole in the preheated oven for 35 minutes; then toss to ensure all components are cooked evenly. Place back in oven, and bake for an additional 30-35 minutes.