Preheat oven to 425°. Peel butternut squash, scoop out seeds, and cut into 1" cubes. Core the apple and chop into about 8 large chunks. Cut onion into similarly large chunks. Put everything on a large baking sheet or roasting pan and sprinkle with salt, pepper, and thyme. Toss with olive oil. Roast for about 25 minutes, until tender, stirring and flipping halfway through.

Allow fruit to cool for a few minutes. Puree with a food processor, blender or immersion blender and season to taste with salt and pepper. Serve warm or cover and reheat in the microwave when ready to eat.