Preheat your oven to 375°F (190°C). Bring a large stockpot of generously salted water to a rolling boil. Add jumbo pasta shells and cook 1-2 minutes LESS than package directions until firm al dente (about 9 minutes).
Drain shells gently and rinse under cool water to stop the cooking process. Arrange them in a single layer on an oiled rimmed baking sheet so they do not tear or stick together.
In a skillet over medium heat with 1 tsp olive oil, wilt the baby spinach for 2 minutes. Transfer to a clean tea towel and squeeze firmly until zero moisture drips out. Finely chop the dry spinach.
In a large mixing bowl, combine whole-milk ricotta, wrung chopped spinach, beaten egg, minced garlic, 1/2 cup grated Parmigiano-Reggiano, 1 cup shredded mozzarella, sea salt, black pepper, and freshly ground nutmeg. Stir until velvety and homogeneous.
Spread 1.5 cups of marinara sauce evenly across the bottom of a 9x13-inch ceramic baking dish. Spoon 1.5 to 2 tablespoons of filling into each cooked jumbo shell (or pipe using a gallon Ziploc bag with a clipped corner). Arrange shells snugly in rows in the dish.
Spoon remaining marinara lightly over and around the shells, leaving bits of creamy filling exposed. Scatter the remaining 1 cup of mozzarella and 1/4 cup of parmesan evenly over the top.
Cover loosely with tented aluminum foil (so cheese doesn't stick) and bake at 375°F for 25 minutes. Remove foil and bake an additional 10 minutes until cheese is bubbly and golden-brown. Garnish with fresh basil and rest 5 minutes before serving.