Preheat the oven to 350 degrees. Grease a 9 x 13 inch casserole dish.
Bring a large pot of salted water to a boil. Add rigatoni and boil about 1 minute less than the al dente package instructions. Drain, then place in the prepared baking dish.
Heat the oil in a large, deep skillet or Dutch oven over medium heat. Add the beef, breaking it up with a spoon and spreading it over the pan. Cook for about 3 minutes, then stir and add the onion. Continue to cook, stirring occasionally, another 6-7 minutes, or until onion is softened and beef is cooked through. Add garlic and saute until fragrant, about 1 minute. Drain off any excess grease.
Stir in the parsley, fennel, and red pepper flakes. Season to taste with salt and black pepper.
Pour in both cans of marinara sauce. Sprinkle with basil and oregano. Stir well and heat through.
Pour the sauce mixture over the pasta in the baking dish, stirring to coat. Sprinkle with cheese, then bake for 23-27 minutes or until cheese is fully melted and starting to brown in places.