Preheat and prep: Heat your oven to 375°F (190°C). Grease a 9x13-inch baking dish or a large oven-safe skillet.
Cook the meat: Warm olive oil in a skillet over medium heat.
Add Italian sausage (or ground beef), breaking it up as it cooks. Season with salt, pepper, and Italian seasoning. Stir in garlic and cook until fragrant, about 30 seconds.
Drain excess fat if needed.
Make the creamy base: In a mixing bowl, whisk the eggs until smooth. Add softened cream cheese and beat until mostly combined. Stir in 1 cup mozzarella and the Parmesan.
It won’t be perfectly smooth—small bits are fine.
Combine base and meat: Fold the cooked meat into the egg-cheese mixture. If using low-moisture add-ins like olives or pre-sautéed mushrooms, fold them in now.
Build the casserole: Spread the mixture evenly into your prepared dish. Spoon the marinara over the top in an even layer.
Sprinkle with remaining 1 cup mozzarella.
Add pepperoni: Arrange pepperoni slices over the cheese. Top with a pinch of red pepper flakes if you like a little heat.
Bake: Place in the oven for 20–25 minutes, until the edges are set and the cheese is melted and lightly browned. For extra color, broil on high for 1–2 minutes at the end, watching closely.
Rest and serve: Let it rest for 5–10 minutes so it sets.
Slice into squares and serve hot.