Preheat oven to 375 degrees. Spray an 8" X 8" baking pan with nonstick spray.
Bring an extra-large skillet sprayed with nonstick spray to medium-high heat. Cook and stir onion until mostly softened, about 5 minutes. Add spinach, and cook and stir until just wilted, about 1 minute.
Transfer veggies to a large bowl. Let cool for 5 minutes.
Add remaining base ingredients, and mix well. Transfer to the baking pan. Bake until center is firm, about 45 minutes.
Meanwhile, in a medium bowl, mix all topping ingredients except Parm and pepperoni.
Spread seasoned tomatoes over the egg bake, and top with Parm and chopped pepperoni.
Bake until the toppings are hot, about 5 minutes.