Preheat your oven to 375°F (190°C) and lightly grease a 9x9-inch baking dish.
In a large mixing bowl, combine the cottage cheese, shredded mozzarella, grated Parmesan, and the large egg. Add in the Italian seasoning, garlic powder, onion powder, salt, and black pepper. Mix everything together until well combined.
Spread half of the cottage cheese mixture evenly in the bottom of your prepared baking dish.
Pour the marinara sauce over the cottage cheese layer, spreading it out evenly. Sprinkle your sliced pepperoni or any other toppings you prefer over the marinara sauce. Spoon the remaining cottage cheese mixture over the toppings and gently spread it to cover everything.
Place the baking dish in the preheated oven and let it bake for 30-35 minutes until the top is golden brown and bubbly. Let it cool for about 5 minutes before slicing.