Bring a large pot of water to boil and cook the shells according to package instructions.
As the shells boil, prepare the filling: In a large sauté pan, warm the olive oil over medium heat and sauté the garlic. Add the spinach to the pan, toss to coat, and cook just until wilted. Add the fresh basil and season with salt, pepper, and a dash of nutmeg. Drain any extra moisture.
Add the spinach, drained cottage cheese, ricotta, red pepper flakes, and two eggs to a bowl and mix until the filling is a uniform consistency.
Line a roasting pan with a thin layer of marinara.
Stuff the cooked shells with the spinach filling and place in the roasting pan.
Ladle more marinara over top of the entire pan, and cover with aluminum foil.
Bake at 375 degrees for 30 minutes. After 30 minutes remove the foil, adjust the oven temperature to 400 degrees, and bake for an additional 15 minutes.
Serve hot with extra marinara on the side and grated Parmesan over top.
For Homemade Marinara
Bring the olive oil to med-high heat.
Throw in the garlic, parsley, and basil, and cook a minute or two until garlic is browned.
Throw in the chopped tomatoes and their juices, and season with salt and pepper.
