Cook the pasta shells according to package instructions until al dente. Drain and set aside to cool slightly.
In a large skillet over medium heat, add the chopped onion and garlic. Sauté until the onion is translucent. Add the ground beef or turkey, cooking until browned. Drain any excess fat.
In a large bowl, combine the cooked meat mixture with ricotta cheese, mozzarella cheese, Parmesan cheese, Italian seasoning, salt, and pepper. Stir until well mixed.
Carefully fill each pasta shell with the meat and cheese mixture, using a spoon or piping bag for ease.
Spread a thin layer of marinara sauce on the bottom of a baking dish. Arrange the stuffed shells in the dish, seam side up. Pour the remaining marinara sauce over the stuffed shells, ensuring they are evenly covered. Sprinkle additional mozzarella cheese on top.
Cover the dish with aluminum foil and bake in the preheated oven for 25 minutes. Remove the foil and bake for an additional 10 minutes, or until the cheese is bubbly and golden.
Remove from the oven and let it cool for a few minutes. Garnish with fresh basil leaves if desired and serve hot.