Preheat oven to 400° F.
Grease a 12 inch cast iron skillet over medium heat with olive oil. Add onion and cook until lightly brown for 6-7 minutes. Add garlic, pepper flakes and sausage. Break sausage into smaller pieces with a wooden spoon and cook for 6 minutes.
Add the tomatoes and 3 tablespoons of water. For 8 minutes, cook over medium-low heat. Transfer to a bowl.
In another bowl, combine ricotta, egg yolk, thyme, oregano, salt and pepper.
In a third bowl, mix the shredded mozzarella with the parmesan cheese.
In the empty skillet, spread 1 cup of sauce. Put 7 noodle halves around the edge of the skillet and one in the middle. Add 1/3 of the ricotta mixture over the noodles. Then add the mozzarella cheese mixture over the ricotta. Pour 1/3 of the remaining sauce over the mozzarella. Repeat these steps two more times to build up the layers.
Put the skillet into the oven and bake for 30-35 minutes, until the cheese is golden brown. Top with fresh basil and serve.