Prepare rotini according to package directions and drain.
In a skillet over medium heat sauté onions and red and green bell peppers until they are soft.
Add in chicken sausage and cook until browned.
Reduce the heat and stir in the spaghetti sauce and pepperoni. Add in pasta and stir. Add crushed red pepper, if desired.
Spoon half mixture in a 9 x 13 baking dish. Cover with half of cheese. Spoon remaining pasta mixture over the cheese and spread evenly. Sprinkle the remaining cheese evenly over the top.
Bake at 350 degrees for about 25 to 30 minutes or until the casserole is heated through and the cheese is melted.