Preheat and prep: Heat your oven to 375°F (190°C). Lightly grease a 9x13-inch baking dish.
Cook the pasta: Boil the high-protein pasta in salted water. Cook it 1–2 minutes less than al dente so it stays firm after baking.
Drain and set aside.
Sauté the veggies: In a large skillet, warm the olive oil over medium heat. Add onion, bell pepper, and mushrooms. Cook for 5–6 minutes until softened.
Stir in garlic and cook 30 seconds more.
Brown the meat: Add ground turkey (or your choice of meat) to the skillet. Season with salt, black pepper, oregano, basil, and red pepper flakes. Cook, breaking it up, until browned and no longer pink.
Stir in the sauce: Pour in the marinara.
Simmer 2–3 minutes to meld flavors. Taste and adjust seasoning.
Blend the creamy layer: In a bowl, mix the ricotta, blended cottage cheese, 1/2 cup mozzarella, and Parmesan. Season with a pinch of salt and pepper.
Combine: In a large mixing bowl, add the cooked pasta and meat sauce.
Fold together until coated.
Assemble the casserole: Spread half the pasta mixture in the baking dish. Dollop and spread the ricotta-cottage cheese mixture over it. Layer with half the turkey pepperoni.
Add the remaining pasta, then top with the remaining mozzarella and the rest of the pepperoni.
Bake: Cover loosely with foil and bake for 20 minutes. Remove foil and bake another 10–12 minutes, until the cheese is melted and bubbling with golden spots.
Rest and serve: Let it rest 5–10 minutes so it sets. Garnish with fresh basil if you like.
Slice and serve warm.