In a saucepan, warm olive oil over medium heat. Sauté the finely chopped onion until translucent, about 3-4 minutes. Add canned crushed tomatoes, basil, and red pepper flakes; simmer gently for 15 minutes.

Add salt to the marinara sauce if needed before serving.

In a large pot, bring salted water to a boil. Add the manicotti shells and cook until al dente, about 8-10 minutes. Drain and let them cool on a baking sheet.

In a large bowl, combine ricotta cheese, chopped spinach, grated parmesan, egg, minced garlic, nutmeg, and a pinch of salt. Stir until well blended and creamy.

Using a spoon or a piping bag, gently fill each manicotti shell with the ricotta and spinach mixture. Be careful not to overfill, as they can burst during baking!

Spread a thin layer of marinara sauce at the bottom of a baking dish.

Place the filled manicotti shells in the dish, then top with the remaining marinara sauce, covering them evenly.

Preheat your oven to 375°F (190°C). Cover the baking dish with foil and bake for 25 minutes. Remove the foil and bake for an additional 10-15 minutes, until the sauce is bubbly and the top is slightly golden.

Let the manicotti cool for 5 minutes before serving.

Garnish with fresh basil or extra parmesan if desired.

Optional: Drizzle with olive oil for an extra touch of flavor.