Saute beef, onion, and green pepper until beef is no longer pink and vegetables are soft. Add the pepperoni and heat thoroughly. Drain excess grease.
Add spaghetti sauce and simmer 5 minutes.
Spray a 3-qt casserole with cooking spray. Put 1/2 of the pasta in the casserole. Spoon 1/2 of the meat sauce mixture over the pasta. Spoon the container of cottage cheese over the sauce. Sprinkle with 1/2 of the mozzarella cheese.
Top with the remaining pasta, then sauce, then mozzarella cheese.