Bring a large pot of water (about 6 qts) to boil for the pasta. I find peeling and cutting the butternut squash to be the most time-consuming part of the recipe so I recommend you do that first. Cut the ends off, cut the squash in half and then peel, either with a peeler or sharp paring knife. Be careful. Cut in half again, lengthwise, remove the seeds and dice.
Dice the onion and chop up the bacon.
Add the butter to a large saute pan and add the diced onion. Cook over medium heat until golden brown. Add the bacon and cook until it starts to crisp, about 2-3 minutes.
Add the squash and season with salt and pepper. Add the 1 cup of water, stir to combine and cover with a lid for 8-10 minutes until the squash is soft. Check after 5 minutes and make sure all the water has not cooked away. If it has, and the squash is still hard, add more water in 1/4 cup increments until the squash is soft enough to mash with the back of a spoon.
When the water for the pasta comes to a rolling boil, add 2 Tbsp salt and the pound of pasta. Cook until it is al dente, and before draining, reserve about 1/2 cup of pasta water. Drain.
Add 1/4 cup of the reserved pasta water to the sauce, smashing the butternut squash with the back of a large spoon. If it seems too thick, add the other 1/4 cup (I did this). Toss the sauce with the cooked pasta and the grated cheese and serve.
If you'd like to garnish the pasta with some fresh herbs, I think a little sage would be nice. I would have added some if the raccoons had not dug it up out of my garden.