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Preheat oven to 400°F (200°C).
Cut squash in half, leave seeds in and skin on. Put about 1 inch of water and squash (cut side down) in a baking dish. Bake for about 40 minutes or until tender.
Meanwhile, heat oil in a saucepan, add onions and sauté for about 5 minutes. Add rosemary and apples and cook for an additional 8-10 minutes. Season to taste with salt and pepper. Remove from heat and set aside.
When squash is cooked, remove seeds and discard, scoop and fluff up spaghetti. Fill each half with apple mixture. Return to oven and continue to cook for about 10 minutes. Remove from oven and serve.