Preheat oven to 375°F (190°C). Lightly grease a baking dish.
Cook pasta shells in salted water until al dente. Drain and rinse with cool water.
In a large skillet, heat olive oil. Sauté shallot until translucent. Add garlic and cook for another minute.
Add spinach and sauté until wilted. Let cool, then finely chop.
In a bowl, mix ricotta, egg, 1/2 cup mozzarella, Parmesan, nutmeg, salt, pepper, and chopped spinach.
Spread 1 cup marinara sauce on the bottom of the baking dish.
Stuff each shell with the ricotta mixture and place in the dish.
Top with remaining sauce and mozzarella cheese.
Cover with foil and bake for 20 minutes. Remove foil and bake for 10 more minutes until cheese is bubbly and golden.