Preheat the oven to 350 degrees F (175 degrees C). Grease a large baking dish.

Bring a large pot of lightly salted water to a boil. Cook rigatoni in the boiling water, stirring occasionally until tender yet firm to the bite, about 12 minutes. Drain and set aside.

Meanwhile, cook sausage and onion in a large skillet until sausage is no longer pink and onion is translucent, 5 to 7 minutes.

Combine spaghetti sauce, cottage cheese, 1 cup mozzarella cheese, eggs, Parmesan cheese, parsley, Italian seasoning, basil, salt, and black pepper in a large bowl. Add sausage mixture; stir until well combined. Add rigatoni; carefully stir until well incorporated. Transfer to the prepared baking dish; cover.

Bake in the preheated oven for 45 minutes. Top with remaining 1 cup mozzarella cheese; continue baking, uncovered, until cheese is melted, about 15 minutes.