Preheat oven to 400 degrees and grease 9 x 14 baking dish.
Place each spaghetti squash half cut side down onto baking sheet, and bake for 40 minutes.
Meanwhile, heat ghee in a medium sized skillet. When hot, add shallots and cook for 1 minute. Now add garlic, mushrooms, red bell pepper, salt, pepper, and red pepper flakes. Saute an additional 4-5 minutes.
When squash is done roasting, use a fork to separate strands and place into a large serving bowl. Toss with sautéed mushroom red pepper mixture, basil and goat cheese, and season with more salt and pepper if needed.