Bring a large pot of salted water to a boil and cook the jumbo shells until just al dente. Drain and set aside to cool slightly.
In a mixing bowl, combine the spinach, artichoke hearts, ricotta, half the mozzarella, and the Parmesan. Season with salt and pepper, then stir until evenly mixed.
Heat the olive oil in a large skillet over medium heat. Add the onion and cook until softened, then stir in the garlic and cook for one minute more.
Pour in the crushed tomatoes and simmer for 10 minutes. Stir in the heavy cream and season with salt and pepper. Remove from heat.
Spoon the spinach mixture into each cooked shell. Spread a thin layer of sauce in the bottom of a baking dish, then arrange the stuffed shells on top.
Pour the remaining sauce over the shells and sprinkle with the rest of the mozzarella. Bake at 375°F for 25 minutes until the cheese is melted and bubbly.
Let the dish rest for five minutes, then scatter fresh basil over the top before serving.