Preheat oven to 425 degrees F.
Toss butternut squash with olive oil, rosemary, salt, and pepper.
Place on baking sheet and bake in preheated oven for 40-45 minutes, until tender.
While squash is baking, fry up the bacon and cook the pasta.
When bacon and pasta are cooked, combine them in a large bowl.
Get rid of all but 1 tablespoon of bacon grease, then over medium-high heat, add shallots in large skillet.
Cook until translucent, about 5 minutes.
Add flour, stirring well to combine.
Slowly add milk, stirring constantly.
Bring mixture to a simmer, and let simmer for 1 minute to let thick slightly.
Season with ½ teaspoon of salt.
Remove from heat and add 1 ½ cups of the cheese, stirring to combine.
Add butternut squash to bowl with pasta and bacon, then pour cheese sauce over and toss to combine.
Pour pasta into 9x13" baking dish and top with remaining ½ cup of cheese.
Bake in preheated oven for 10 minutes, or until cheese on top is melted.
Serve and enjoy!