Combine pasta, onion, tomatoes, basil, and 1 cup of the mozzarella in the baking dish. Give it a couple stirs to distribute ingredients evenly. Then, spread remaining cup of mozzarella evenly across the top. Sprinkle with a salt, pepper, and more fresh basil if desired.
Bake at 375 for 35 minutes or until tomatoes start to collapse and cheese is completely melted and bubbling.