Preheat the oven broiler.
Beat eggs, salt, and pepper together in a medium bowl.
Melt ghee in a large cast iron skillet over medium heat. Add the onion and sauté until translucent, approximately 5-6 minutes.
Add the squash, zucchini, and fresh thyme and continue to cook until squash begins to tender.
Add the mushrooms and tomatoes and sauté for a few more minutes.
Add garlic and cook until fragrant, approximate 30 seconds.
Pour in the egg mixture and reduced heat to low. Cook until the eggs begin to set.
Sprinkle the green onions on top and transfer the skillet to the oven. Broil until eggs just begin to brown, approximate 5 minutes.
Slice into wedges and enjoy!