Heat oven to 375°F. Lightly grease a 9x13-inch baking dish.
Boil rigatoni in salted water until very al dente, about 2 minutes shy of package time. Reserve 1/2 cup pasta water and drain.
Warm olive oil in a large skillet over medium heat. Brown the sausage, breaking it up, 6 to 8 minutes. Drain excess fat.
Stir in onion and cook until translucent, 4 to 5 minutes. Add garlic and cook 30 seconds.
Mix in tomato paste and cook 1 minute. Pour in marinara and the reserved pasta water. Season with oregano, red pepper flakes, 1 tsp salt, and black pepper. Simmer 5 to 8 minutes, then stir in half the basil.
In a bowl, combine ricotta, 1 cup mozzarella, and 0.25 cup Parmesan with a pinch of salt and pepper.
Toss the drained rigatoni with the sausage sauce until evenly coated.
Spread a thin layer of sauce in the baking dish. Add half the pasta, dot with half the ricotta mixture, and sprinkle with 1 cup mozzarella and 0.25 cup Parmesan.
Repeat with remaining pasta and ricotta. Top with the rest of the mozzarella and Parmesan.
Cover with foil and bake 15 minutes. Uncover and bake 10 to 12 minutes more until bubbly and lightly browned. Rest 10 minutes, then garnish with remaining basil.