Cut 2 small slits on each side of the spaghetti squash. Microwave for 4 minutes. Let cool until the squash is easy to handle.
Cut spaghetti squash in half and scoop out all the seeds. Place on a baking sheet skin side down.
Lightly spray each half with cooking spray. Evenly spread half of the salt and pepper and all of the cayenne and garlic powder to the squash. Add 1 spring of thyme to each half and bake for 35-45 minutes. You will know when the squash is done when you can poke the inside with a fork and the strands will pull easily but are still firm in shape.
While the spaghetti squash is cooling, add bacon to a deep saute pan and cook until brown. Remove the bacon and place on a paper towel to absorb excess grease but leave as much of the drippings in the pan as you can.
While bacon is cooking, gently use a fork and scrap out the insides of the spaghetti squash. Set aside.
Add garlic, shallots, remaining thyme, and crushed red pepper to the pan. Cook for 4-5 minutes on medium heat until the garlic and shallots are translucent. Add spaghetti squash, salt, and pepper. Cook for 5 minutes, mixing well.
Once spaghetti squash is heated through it is ready to eat. Top with bacon and grated Parmesan cheese. Enjoy!
Notes
Typically I prefer shredded Parmesan cheese over grated but for this recipe the grated makes a big difference in the taste of the dish.
This dish makes wonderful leftovers. Simply microwave or reheat in a pan the next day. I would recommend keeping the bacon separate until you are ready to eat because it will get soggy if premixed with the squash.
If you don't have fresh thyme you can substitute with 1/4 tsp dried thyme during the baking process and just skip the thyme during the saute steps. You can also experiment based on what you have on hand. I get a lot of fresh herbs from my garden and I've loved this recipe with thyme, oregano, and rosemary.
Looking to make this vegetarian? No problem! Just omit the bacon and use either olive oil to saute or a little vegetable stock for a low fat/calorie option.