1. Preheat the oven to 375°F and lightly grease a large baking dish.

2. Bring a large pot of salted water to a boil and cook the manicotti shells until slightly under al dente. Drain carefully and place on an oiled surface to prevent sticking.

3. Heat olive oil in a skillet over medium heat. Add onion and cook until softened. Stir in garlic and cook until fragrant.

4. Add spinach to the skillet and cook until wilted. Remove from heat and allow the mixture to cool slightly.

5. In a large bowl, combine ricotta cheese, 1 cup mozzarella cheese, Parmesan cheese, egg, spinach mixture, parsley, basil, Italian seasoning, salt, black pepper, and red pepper flakes.

6. Spread 1 cup of marinara sauce across the bottom of the prepared baking dish.

7. Transfer the ricotta filling into a piping bag or zip-top bag and carefully fill each manicotti shell.

8. Arrange the stuffed manicotti shells in the baking dish in a single layer.

9. Pour the remaining marinara sauce evenly over the pasta shells.

10. Sprinkle the remaining mozzarella cheese over the top.

11. Cover the baking dish with foil and bake for 30 minutes.

12. Remove the foil and continue baking for 10 to 15 minutes until the cheese is golden and bubbly.

13. Let the manicotti rest for 10 minutes before serving.

14. Garnish with fresh basil, parsley, or extra Parmesan cheese before serving warm.