Preheat oven to 375º. Lightly coat a 9x13 baking dish with cooking spray and set aside.
Cook pasta according to package directions.
While the pasta is cooking, place cubed butternut squash in a microwave-proof bowl and cover with plastic wrap. Microwave for 4 minutes, or until squash is cooked through and fork tender. Carefully remove the plastic wrap and mash squash. Set aside.
Heat butter in a medium saucepan over medium-high heat. Add mushrooms and green onions. Cook until tender, about 5 minutes. Sprinkle flour over mushroom mixture and stir for 1 minute. Add milk and salt & pepper. Cook and stir over medium heat until thickened and bubbly. Remove from heat and stir in squash.
Drain pasta when cooked and add to mushroom and squash mixture. Gently fold to combine. Pour half of the pasta mixture into the prepared dish. Sprinkle with half of the cheese. Pour the rest of the pasta mixture on top and then sprinkle the remaining cheese over it.
Bake uncovered for 20-25 minutes or until heated through and cheese is melted. Serve and enjoy!