Preheat oven to 375°F (190°C). Lightly grease a 9x13-inch baking dish with olive oil.

Bring a large pot of salted water to a boil. Cook rotini 1 minute less than package directions (about 9 minutes). Drain and set aside. The pasta will finish cooking in the oven.

While pasta cooks, heat 1 tablespoon olive oil in a 12-inch skillet over medium-high heat. Add ground beef and cook, breaking it apart, until browned (about 5 minutes). Drain excess fat, leaving about 1 tablespoon in the skillet.

Reduce heat to medium. Add diced onion and cook until softened, about 3 minutes. Stir in garlic and cook 30 seconds until fragrant.

Pour in marinara sauce. Add oregano and red pepper flakes if using. Season with 1/2 teaspoon salt and 1/4 teaspoon black pepper. Simmer for 5 minutes, stirring occasionally.

In a large bowl, combine cooked rotini, meat sauce, and half the pepperoni. Toss until evenly coated.

Transfer mixture to the prepared baking dish. Spread into an even layer. Sprinkle mozzarella over the top, then arrange remaining pepperoni slices on the cheese. Sprinkle Parmesan on top.

Bake uncovered for 18-20 minutes, until the cheese is melted and bubbly with golden brown spots. For a browner top, switch to broil for the last 2 minutes, watching carefully to avoid burning.

Let rest for 5 minutes before serving. The casserole will set slightly, making it easier to scoop.