Preheat the oven to 375 degrees F and lightly coat a large casserole dish with avocado oil or olive oil.
Cook the bacon in a large skillet over medium-high, flipping every 2 to 3 minutes, until much of the fat has rendered and the bacon reaches desired done-ness. Transfer the bacon to a cutting board and leave the skillet on the stove top. Reduce heat to medium.
Place the chopped butternut squash in the skillet and cover. Cook, stirring occasionally, for 3 minutes. Remove cover and add spinach. Cook, stirring occasionally, until spinach has wilted, about 3 minutes.
Stir in the oregano, chives, and sea salt. Chop the bacon and add it in as well. Transfer this mixture to the prepared casserole dish.
Whisk the eggs together in a mixing bowl until creamy. Pour the beaten eggs over the vegetables and use a spoon to gently stir to evenly distribute the vegetables. Evenly sprinkle the cheese over the casserole.
Bake on the center rack of the preheated oven 45 to 55 minutes, until casserole tests clean (mine takes 50 minutes).
Allow casserole to cool 10 minutes before slicing and serving. Serve with plain yogurt (I use coconut milk yogurt), sour cream, chopped chives, and any other toppings you desire.