Preheat the oven to 350 degrees. Spray a large casserole dish or Pyrex 9 by 13 pan with cooking spray. Heat the olive oil in a large skillet. Once hot, add the onion, cook until soft. Add in garlic, mushrooms, and red peppers. Remove from heat and cool.
In a large bowl combine the ricotta, 1/4 cup of the mozzarella, 1/4 cup of the Parmesan, stir well. Add in the egg, spinach, dried basil, crushed red pepper,salt and fresh cracked pepper to taste. Mix well until creamy. Add the mushroom, onion, red pepper mixture.
Pour 1/2 cup of marinara sauce in the bottom of your sprayed baking dish. Place the cooked shells in the pan. Make sure they are spaced out evenly. Stuff each shell with cheese/veggie mixture. Use a spoon, it might get messy:)
Pour the remaining sauce over the stuffed shells. Add the leftover mozzarella and Parmesan.
Cover with foil and bake for 30 minutes. Remove the foil and bake for an additional 5 minutes. You want the shells to be bubbling with goodness. Let cool for a few minutes and serve warm.