Preheat the oven to 375°F. Halve the butternut squash and use a spoon to scoop out the seeds. Then, using a vegetable peeler, remove the skin.
Cut into ¼” strips, and then again into small cubes. Place the butternut squash cubes on the baking pan and toss in cooking oil, salt, and pepper. Bake for 35 minutes.
Melt butter in a sauce pot over medium heat. Add the butternut squash, fresh thyme leaves, hot sauce, and pasta water, nutritional yeast and cheese. Blend with immersion blender.
Pour your noodles in dish. Then, add vegetable mixture, butternut squash cheese sauce and crackers over top.
Bake for 15-18 minutes or until dish is hot and cheese is melted. Broil for 2-3 minutes for a bubbly, cheesy bake! Enjoy!