Preheat the oven to 400ºF and line a baking sheet with parchment paper.
Next prepare the spaghetti squash. Use a large, sharp knife to carefully slice the spaghetti squash in half lengthwise (hotdog style). Remove the innards of the spaghetti squash out with a spoon.
Drizzle about 2 teaspoons of olive oil over each half of the spaghetti squash and then season with ¼ teaspoon of salt and ¼ teaspoon of ground pepper.
Place the spaghetti squash open side-down on the lined baking sheet and bake for 20 minutes at 400ºF.
While the spaghetti squash is baking, prepare the mac and cheese topping. Add the corn flakes to a food processor and process until the corn flakes look like breadcrumbs. Add garlic powder, thyme, parsley, red pepper flakes, salt and mozzarella cheese to the food professor and pulse until just combined. Set aside for later.
After 20 minutes, flip each half of the spaghetti squash over and bake for another 20 minutes. We recommend checking the squash with a fork after 10 minutes to make sure your spaghetti squash isn’t getting mushy. Every oven is different so the time may vary.
While the spaghetti squash is baking, prepare the cheese sauce by making a roux. Heat a small saucepan over medium/high heat. Add butter. When the butter is melted add the cracked pepper corns to the butter. When the pepper is fragrant, add flour and whisk until the butter and flour form a paste. Cook the paste for about 1 minute.
Slowly add milk to the pot, whisking constantly. Continue to whisk the roux over medium heat for about 4-6 minutes or until the roux thickens.
When the roux is thick, remove from heat and add the gouda cheese and mozzarella cheese. Stir until the cheese has melted.
Add the hot sauce and salt to the cheese sauce and mix again to combine. Set cheese sauce aside.
Remove the spaghetti squash from the oven and let it rest for 5 minutes before carefully “fluffing” the edges of the squash with a fork to loosen the spaghetti squash from the skin of the skin.
Turn the heat on the oven to broil.
Pour half of the cheese sauce into each half of the fluffed spaghetti squash and gently toss the “spaghetti squash noodles” with the sauce until they are coated.
Top each spaghetti squash half with 2-3 tablespoons of the corn flake topping and drizzle the olive oil over the tops of each squash. Place the squash in the oven and broil for 1-2 minutes or until golden brown. Be sure to keep an eye on the squash as every broiler is different.
Remove the squash from the oven and enjoy.