Preheat the oven to 375 degrees F. Spray a 9-inch x 13-inch baking dish with non-stick cooking spray. Set aside.
Bring a large pot of salted water to a boil. Add the rotini and cook according to the package directions until al dente, about 8 minutes. Drain the water and return the pasta to the pot.
Add the spaghetti sauce, 2 cups of mozzarella, 1 cup of pepperoni, half of the onion, and half of the bell pepper. Stir to combine.
Pour the pasta mixture into the prepared baking dish and spread into an even layer.
Sprinkle 1 cup of mozzarella on top of the pasta. Layer the remaining pepperoni, onion, and bell pepper on top of the cheese. Then, sprinkle the remaining 1 cup of mozzarella over the casserole.
Bake for 10 to 15 minutes or until cheese is melted and bubbly. Remove from the oven and serve warm.