Cut the spaghetti squash in half and remove the seeds. Place in a covered dish with a ¼ inch of water and microwave for 10 -12 minutes. In a medium sized skillet over medium heat, add the butter, onions, red pepper and thyme and cook until the onions are slightly brown in color. Salt and pepper to taste.
Using a fork, scrape the insides of the squash and transfer to a small bowl. Combine the squash, onions, sour cream and half the cheese together and mix well. Transfer the mixture to a buttered baking dish and top with remaining cheese.
Place into a 375º for 15 – 20 minutes until golden brown on top.