Cook shell pasta in a large pot with boiling salted water until al dente. Drain well.
In a large skillet brown the ground beef and onions. Drain grease.
In a large bowl add the chopped tomatoes, tomato sauce, and cottage cheese; stir well. Add basil, oregano, garlic, salt, and pepper to taste. Stir until well blended.
In the bottom of a 2 quart baking dish, cover with a half of cup of tomato sauce mixture. Stuff shells with beef mixture and place side by side in dish. Cover stuffed shells with remaining tomato sauce and top with mozzarella cheese. Cover with aluminum foil.
Bake at 350 degrees F (175 degrees C) for an hour. Allow to stand for 15 minutes and serve.