Preheat oven to 400 degrees. Cut the spaghetti squash in half lengthwise, and remove the center seeds and guts. Drizzle with olive oil and season with salt and pepper. Place face down on a large baking sheet lined with foil. Bake for about 45 minutes or until tender and slightly browned on the edges.
Remove from oven. Using a thongs and fork, scrape out the squash and place into a bowl and set aside.
Line a large baking sheet with parchment paper. Form each slice of prosciutto into a nest on the baking sheet. Bake in the 400 degree oven after squash is done for 10-15 minutes, or until it begins to crisp. Watch closely so it does not burn. Chop or break into chunks.
While the squash is roasting, slice the onions and place in a large skillet with olive oil. Season with salt and pepper. Cook on medium for about 30 minutes, stirring occasionally. After 30 minutes the onions should be slightly browned and cooked. Stir in 1 tbsp of balsamic vinegar. Once it is reduced add in another tbsp, and repeat one more time after that, totaling 3 tablespoons. Remove onions from pan and onto a plate, set aside.
Using the same skillet you cooked the onions in (that have been removed), add the butter and minced garlic over medium heat, whisk for about 2 minutes. Whisk in the flour and cook for another 2 minutes. It will be a bubbly paste. Slowly whisk in the milk. It should thicken quite fast, add in the brie cheese. Whisk until all of the cheese is melted. It may look like a gloppy cheesy blob, but that's OK!
Add the spaghetti squash into the cheese sauce. Stir to coat all the squash. Stir in the balsamic onions. Season with salt and pepper to taste. Add some red pepper flakes for an added kick. Top each serving with crumbled crispy prosciutto and fresh parsley. Enjoy!