Preheat your oven to 350 degrees.
Set aside 1/2 oz pepperoni and roughly chop up the remaining pepperoni (1oz) and all the basil. Set aside in a bowl.
Make 3-4 slices off the tomato lengthwise and chop the remaining tomato into small chunks. If desired, slice the mushroom lengthwise into thin slices (optional for topping).
Crack the eggs in a large mixing bowl, add the salt, oregano, red pepper flakes and black pepper and whisk to combine.
Add in the chopped up pepperoni, basil, and tomato chunks (leaving the 1/2 oz pepperoni, and tomato and mushroom slices aside). Add in the cheese and whisk to combine.
Heat a large (12 inch) skillet to medium high heat. Once hot pour in the egg mixture and allow to cook for 2-3 minutes until you can scrape a spatula along the edges. If the eggs start to bubble, turn the heat down to medium.
Once the edges have cooked and slightly pulled away lay on the slices of pepperoni, tomato and mushrooms, and place in the oven. Bake for 15-20 minutes (time varies oven to oven).
Enjoy! Store in a zip top bag or sealed container up to 1 week.