Bring a large pot of salted water to boil and cook pasta shells according to package directions until al dente, about 9-10 minutes. Drain and rinse with cold water, then set aside.

Preheat your oven to 375°F (190°C). Lightly grease a 9x13 inch baking dish with butter or cooking spray.

In a large mixing bowl, combine ricotta cheese, 3/4 cup Parmesan, 1/2 cup mozzarella, egg, chopped sage, minced garlic, salt, pepper, and nutmeg. Mix gently until all ingredients are well incorporated.

Using a small spoon or piping bag, carefully fill each cooked pasta shell with the ricotta mixture, about 2-3 tablespoons per shell. Place stuffed shells in the prepared baking dish in a single layer.

In a medium saucepan, melt butter over medium heat. Add whole sage leaves and cook for 2-3 minutes until leaves are crispy and butter is fragrant. Remove sage leaves and set aside for garnish.

Add heavy cream to the sage butter and stir to combine. Add pasta cooking water to thin the sauce slightly. Season with salt and pepper. Bring to a gentle simmer, then remove from heat.

Pour the sage cream sauce evenly over the stuffed shells in the baking dish, making sure to coat all shells.

Combine remaining mozzarella and Parmesan cheese, then sprinkle evenly over the shells.

Cover the baking dish with aluminum foil and bake for 25 minutes. Remove foil and bake for an additional 10-15 minutes until cheese is melted, bubbly, and golden brown on top.

Remove from oven and let rest for 5 minutes before serving. Garnish with reserved crispy sage leaves and additional Parmesan if desired.