Preheat oven to 375 degrees Fahrenheit (190 degrees Celsius) and grease a 9x13 inch baking dish.
Bring a large pot of salted water to a boil and cook rotini pasta for 2 minutes less than the package instructions for al dente.
In a large skillet over medium-high heat, brown the Italian sausage, breaking it into small crumbles until no longer pink.
Add the diced onion to the skillet and sauté for 5 minutes until translucent; add minced garlic and cook for 1 minute more.
Stir the marinara sauce, dried oregano, and red pepper flakes into the sausage mixture and simmer for 5 minutes.
Drain the pasta and return it to the pot; stir in the sausage and sauce mixture along with the ricotta cheese until well combined.
Transfer half of the pasta mixture to the prepared baking dish and sprinkle with 1 cup of mozzarella cheese.
Add the remaining pasta mixture and top with the remaining 1 cup of mozzarella and the parmesan cheese.
Bake for 20 to 25 minutes until the cheese is melted and bubbling.
Garnish with chopped fresh parsley before serving.