Preheat oven to 400 degrees Fahrenheit.
Cut squash in half, longways and scoop out seeds.
Drizzle squash halves with olive oil and sprinkle with salt and pepper. Bake for 45-60 minutes, or until fork tender. Set aside to cooled enough to handle.
Boil pasta in salted water until two minutes short of al dente, according to pasta package instructions, drain and rinse with cold water. Set aside.
Fry bacon until crispy, drain on paper towels and set aside.
Crush pretzels in a plastic zip lock bag using a rolling pin until they resemble breadcrumbs.
In the same pot that the pasta was boiled in fry the sage leaves in butter on medium high heat until fried and crispy, remove the leaves.
Add flour to the butter that the sage was fried in and whisk until thick paste, or roux, has formed.
Pour in chicken stock, whisk, and simmer until thickened and flour taste is no longer present, about 5 minutes.
Reduce heat to low and stir in the milk.
Scoop the soft, cooked flesh out of the roasted squash and add to the pot of stock mixture.
Use an immersion blender, or transfer to a blender or food processor and blend/pulse on medium speed until smooth.
Fold in the shredded cheese and cream cheese and stir on low heat until smooth.
Salt and pepper to taste.
Fold in the cooked macaroni pasta and bacon.
Pour into a 13x9 inch, or similarly sized casserole dish.
Top with fried sage and crushed pretzel breadcrumbs.
Bake for 20-30 minutes until golden brown.