Boil the pasta according to the directions, reserving 1/2 cup of pasta water before draining. Set aside the pasta. In a large pot, brown the beef along with the onion and garlic. Put the can of tomatoes in a bowl and break them up with your hands until the tomatoes are properly crushed. Add the tomatoes, oregano, thyme, salt, and pepper to the beef mixture. In a separate bowl, mash the beans, adding 1/4 cup of the pasta water to the beans and if the beans are still really thick, or if you are having a hard time mashing and mixing them, add more water until the mixture is sort of smooth. It can still have some chunks in it, you just want it to look more like a loose paste than beans. Take the bean mixture and stir it into the the pot with the beef and tomatoes. Simmer the sauce for about 20 minutes. Remove from heat. Then add the basil and the Pecorino Romano. Then fold in the pasta.

Preheat the oven to 375 degrees F. In a greased 9 x 13 inch casserole dish, pour the pasta mixture from the pot. Top with Mozzarella. Cover with foil and bake for 35 minutes, removing the cover for the last 10 minutes. Remove from the oven and allow the casserole to cool for about 15 minutes before serving.