Cut the spaghetti squash in half & remove the seeds. Place in a covered dish with a ¼ inch of water & microwave for 10 -12 minutes.
In a medium sized skillet over medium heat, add the butter, onions, red pepper & thyme & cook until the onions are slightly brown in color. Salt & pepper to taste.
Using a fork, scrape the insides of the squash & transfer to a bowl. Combine the squash, onions, sour cream, cream cheese & half the cheese together & 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.