Preheat oven to 375°F. Cook pasta shells according to package directions until al dente. Drain and set aside to cool slightly.
In a large bowl, combine ricotta cheese, pumpkin puree, 1 cup mozzarella, Parmesan, egg, sage, nutmeg, garlic, salt, and pepper. Mix until well combined.
Spread 1 cup of marinara sauce on the bottom of a 9x13-inch baking dish.
Fill each shell with about 2 tablespoons of the pumpkin-ricotta mixture and arrange in the baking dish.
Pour remaining marinara sauce over the shells and sprinkle with remaining ½ cup mozzarella cheese.
Cover with foil and bake for 25 minutes. Remove foil and bake an additional 10 minutes until cheese is bubbly and golden. Let rest 5 minutes before serving.