1. Preheat your oven to 400°F (200°C). Carefully cut the spaghetti squash in half lengthwise and scoop out the seeds.
2. Drizzle the inside of each squash half with olive oil and season with salt and pepper. Place them cut-side down on a baking sheet and roast for 35-40 minutes, or until tender.
3. While the squash is roasting, heat a skillet over medium heat and add a splash of olive oil. Sauté the onion until translucent, about 5 minutes.
4. Add the minced garlic to the skillet and cook for another minute until fragrant.
5. Pour in the heavy cream and bring to a gentle simmer. Stir in the Gruyère, Parmesan, and dried thyme, and season with salt, pepper, and optional red pepper flakes.
6. Once the squash is done, let it cool slightly. Using a fork, scrape out the flesh into strands and add them to the cheese sauce. Mix well to combine.
7. Transfer the mixture to a greased baking dish. Top with extra cheese if desired and bake for 15-20 minutes until bubbly and golden on top.

From my experience, the secret to that perfect golden topping is a quick broil for the last two minutes. But keep an eye on it—those precious moments can make all the difference between beautifully browned and slightly burned!