Preheat oven to 400 degrees F. On a baking sheet, toss together half the olive oil, butternut squash, garlic, thyme, and a pinch each of crushed red pepper flakes, rosemary salt, and pepper.
Place the bacon on a separate baking sheet.
The squash will be to roast for about 40-50 minutes.
Cook the bacon for 10 minutes, flip and bake another 5 minutes, until the bacon is crisp. Remove the bacon.
As the squash is roasting caramelize the onions by sautéing on low heat in olive oil, salt, and pepper for 15-20 minutes.
Remove the onions and sauté the mushrooms in 2 tbsp of butter. Allow them to get slightly crispy. Set the mushroom's aside with the onions and bacon that you have chopped.
When the squash is done transfer that and garlic to a food processor. Puree until smooth. Season with salt and pepper.
Boil the pasta until al dente. Before draining, scoop out 1 cup pasta water, then drain the pasta and add the pasta back to the hot pot. Add the butternut squash puree, butter, cheese, caramelized onions, half the bacon (crumbled), mushrooms, onions tossing to combine. Thin the sauce with the reserved pasta water until it reaches your desired consistency.
Divide the pasta between plates. Top with more bacon and cheese.