Preheat your oven to 375°F (190°C). Lightly grease a 9x13 inch baking dish with cooking spray or a small amount of olive oil.

Cook the rotini pasta according to package directions until it is al dente. This usually takes about 8-10 minutes. Drain the pasta well and set it aside.

While the pasta cooks, heat 1 tablespoon of olive oil in a large skillet over medium heat. Add the chopped yellow onion and cook, stirring occasionally, until it softens and becomes translucent, about 3-5 minutes. Add the minced garlic and cook for another minute until fragrant, being careful not to burn it.

Stir in about half (approximately 2.5 oz) of the pepperoni slices into the skillet. Cook for 2-3 minutes, stirring, until the pepperoni starts to crisp slightly and release its oils.

Pour the marinara sauce and 1/2 cup of water into the skillet. Add the Italian seasoning, red pepper flakes (if using), and season with salt and black pepper to taste. Bring the sauce to a gentle simmer, then reduce heat to low.

Add the cooked and drained pasta to the skillet with the sauce mixture. Stir in 1.5 cups of the shredded mozzarella cheese. Mix everything well until the pasta is thoroughly coated with sauce and cheese.

Transfer the entire pasta mixture into the prepared 9x13 inch baking dish, spreading it evenly.

Top the casserole with the remaining 1/2 cup shredded mozzarella cheese and the rest of the pepperoni slices. If desired, sprinkle with grated Parmesan cheese for extra flavor.

Bake in the preheated oven for 20-25 minutes, or until the casserole is bubbly around the edges and the cheese on top is melted and lightly golden brown.

Remove the casserole from the oven and let it stand for 5-10 minutes before serving. This allows the casserole to set slightly, making it easier to serve.