Place oven rack to the middle position. Preheat oven to 400°F.
Place a 12-inch cast iron skillet over medium heat. Add the olive oil. Once the olive oil is shimmering add the onion and cook until lightly browned, about 6-7 minutes. Add the garlic and red pepper flakes. Add the sausage to the onions. Using a wooden spoon break the sausage up into bite size pieces. Cook until no longer pink, about 6 minutes.
Add the fire roasted tomatoes and 3 tablespoons of water to the sausage and onion. Cook over medium-low heat for 8 minutes. Transfer to a bowl.
In a separate medium size bowl, add the ricotta, egg yolk, thyme, oregano, ½ tsp salt, and ½ tsp pepper. Stir to combine.
In a 3rd bowl combine the shredded mozzarella and parmesan.
In the bottom of the empty skillet spread 1 cup of sauce. Add 7 noodle halves around the edge of the skillet and 1 noodle half in the middle. Add 1/3 of the ricotta mixture over the noodles (spread evenly over the noodles), then top with ¼ of the mozzarella cheese mixture over the ricotta. Add 1/3 of the remaining sauce over the mozzarella. Repeat this layering process two more times. Starting with the noodles and ending with the sauce. Sprinkle the remaining mozzarella cheese mixture over top. (See blog post for pictures to illustrate the process).
Transfer the skillet to the oven and bake for 30-35 minutes, or until the edges are bubbling and the cheese is slightly golden brown.
Remove from the oven, top with chopped fresh basil and serve.