Thinly slice the butternut squash and onion, then dice the apple.
Melt butter over medium heat, add the vegetables, and begin sauteing. Season with salt and pepper. Cover and let cook, stirring occasionally so that the squash doesn't stick.
Clean and slice the mushrooms and chop the sage. Add them to the pan with the other ingredients, then sprinkle with brown sugar and mix to combine.
Bring a pot of water to boil and cook gnocchi according to package directions. Once cooked, add directly to the pan with the squash and the desired amount of pasta water.
Take off the heat and serve. If desired, top with toasted walnuts or bacon.