Cook pasta 2 minutes under al dente according to package directions, drain and set aside.
Heat olive oil in a large skillet add onions and saute 2-3 minutes, add sausage and cook stirring occasionally, until cooked through about 12 minutes. Drain fat and add in garlic and cook another 1-2 minutes. Add in sauce and simmer for 10 minutes.
In a medium bowl add cottage cheese, cream cheese, and 2 cups mozzarella cheese, 1 tablespoon chopped fresh basil and mix until combined.
Add meat mixture to pasta and mix until combined. In a 9x13 baking dish pour half the pasta mixture into the baking dish. Add small scoops of the cheese mixture on the pasta. Then add the rest of the pasta. Top with 1 cup mozzarella cheese