Preheat oven to 400 degrees. Halve spaghetti squash and remove seeds. Brush cut sides with 1 Tbsp of oil. Place face down on rimmed baking sheet and bake for 20 minutes. Remove from oven and use fork to remove "spaghetti" strands. Reduce oven temperature to 350 degrees.

In a medium pan, heat remaining 1 Tbsp oil over medium heat. Add onion and garlic and saute for 5 minutes. Added pepper and zucchini. Cook for an additional two minutes. Combine with spaghetti squash in a large bowl.

Spray muffin cups with nonstick cooking spray. Divide vegetable mixture evenly between the muffin cups.

In a large bowl, combine eggs, egg whites, cheese, thyme, crushed red pepper, salt and pepper. Divide between muffin cups.

Bake at 350 for 15 minutes or until eggs are set.