Preheat the oven to 350F and grease a 9" pie pan generously with coconut oil or butter.
Melt one teaspoon of butter in a large skillet over medium heat, and saute the chopped onions for about 10 minutes, until tender and translucent. In another large skillet over medium heat, saute the sliced mushrooms in the other teaspoon of butter and 1/4 teaspoon of sea salt, until they are tender. Remove both the sauteed onions and mushrooms from the heat, and transfer them to a large bowl with the shredded summer squash.
Add the eggs, 3 oz. of shredded cheese, dried thyme and remaining 1/4 teaspoon of sea salt to the bowl, and mix until everything is well combined. Transfer the mixture to the greased pie pan, and top with the remaining ounce of shredded cheese.
Bake at 350F for about 35 minutes, or until golden around the edges and firm in the center.
Remove from the oven and allow to cool for 10 minutes before serving.
Store any leftovers in the fridge, well covered, for up to 4 days.
If you don't care for mushrooms, there are a variety of other veggies you could use instead. Try adding spinach, kale, broccoli, peppers, or any other vegetables you like!