Make the filling:
In a bowl, combine the chopped spinach, ricotta, mozzarella, Parmigiano, egg, salt, pepper, and nutmeg (if using). Mix until fully combined.
Prepare the baking dish:
In a stainless steel or ceramic baking dish, spread 1 cup of marinara sauce over the bottom.
Stuff the shells:
Using a spoon or piping bag, fill each pasta shell with the ricotta-spinach mixture and place seam-side up in the baking dish.
Top and bake:
Spoon the remaining marinara sauce over the shells. Sprinkle with more mozzarella and Parmigiano. Cover loosely with foil.
Bake:
Bake at 375°F (190°C) for 25 minutes covered, then uncover and bake an additional 10–15 minutes until cheese is melted and bubbly. Broil for 2 minutes if you want a golden top.
Serve:
Let rest 5 minutes before serving. Garnish with fresh basil or a drizzle of olive oil if desired.