Beat the eggs in a large bowl. Add the ricotta, 1/2 cup Parmesan, 1/4 cup basil, parsley, and oregano, season with salt and pepper, and stir to combine well. Set aside.
Heat the oil in a large skillet over medium heat. Add the onions and sauté for 5 minutes until tender and golden. Add the garlic and sauté for 1 more minute, until you can smell the garlic. Add the ground turkey and the red pepper flakes, season with salt and pepper, and cook, stirring frequently, until the turkey is cooked, brown, and crumbly. Remove from the heat and cool to room temperature. Add the cooled turkey to the ricotta mixture.
While the turkey cools, bring a large pot of salted water to a boil. Cook the shells according to package directions (there should be a set of instructions for cooking them for a shorter time, if they will be baked later. If not, cook them for 4 minutes less than the full cooking time). Drain the shells and set aside.
Spoon a thin layer of the spaghetti sauce into the bottom of a shallow 3-quart baking dish (a 9x13-inch pan works well). Use a tablespoon to stuff the cooked shells with the ricotta mixture, dividing it evenly between the shells; it’s easiest to stuff the shells while holding them in your hand. Line them up neatly in the prepared pan, following the shape of the pan. Pour the rest of the spaghetti sauce evenly over the stuffed shells. Distribute the mozzarella and remaining 1/4 cup Parmesan over the top of the shells.
Bake the shells for about 20 minutes, until the cheese is melted and turning a bit golden and everything is lovely and bubbling. Let sit for 5 to 10 minutes before serving. Sprinkle with extra slivered basil before serving.
Notes
You can use packaged or fresh mozzarella here. Fresh mozzarella can be grated, or if it’s easier, you can slice it thinly and then chop it on a cutting board into tiny pieces, just the right size for sprinkling on top.
This dish can be made ahead and refrigerated, covered, in the fridge for up to 2 days. The baked shells can be stored in the refrigerator for up to 5 days. Reheat the shells in a 350 over, covered, until hot throughout, about 20 minutes. Or reheat portions in the microwave.
If you want to freeze the casserole, wrap it tightly in plastic wrap and then foil, and label it. Freeze for up to 4 months.
Make sure to remove the plastic before baking it! You can either defrost it in the fridge overnight and then bake as instructed, or if you want to bake it from frozen, remove the plastic, recover the casserole with foil, and bake at 350 degrees for 40 minutes. Then remove the foil and continue baking until hot throughout, the cheese is bubbly, and the top is browned.