Bring a large pot of salted water to a boil. Gently add the manicotti shells and cook for 6-7 minutes until slightly softened. Drain and set aside to cool.
In a mixing bowl, combine ricotta cheese, 3/4 cup mozzarella cheese, Parmesan cheese, the egg, garlic powder, dried basil, onion powder, and red pepper flakes if using. Mix until well combined.
Using a piping bag or a spoon, carefully fill each manicotti shell with the cheese mixture.
Spread 1 cup of marinara sauce on the bottom of a 9x13 inch baking dish. Arrange the stuffed manicotti on top. Pour the remaining marinara sauce evenly over the stuffed shells.
Sprinkle the remaining 1/4 cup of mozzarella cheese on top of the sauce-covered shells.
Cover the dish tightly with aluminum foil and bake for 25 minutes. After that, remove the foil and bake for an additional 15 minutes, or until the cheese is bubbly and golden.
Allow to cool for 5 minutes before serving. Garnish each serving with fresh basil leaves.
Notes
Feel free to add more spices to the filling for extra flavor.