In a saucepan over medium heat, sauté onion until soft. Add garlic, mushroom and spices and continue sautéing until mushrooms reduce in size. Stir in cooked rice and marinara sauce and sprinkle with red pepper flakes and salt and pepper to taste.
While vegetables are cooking, cut peppers in half, removing the seeds and stems. Place the peppers in an oven-proof dish. When the filling is ready, fill peppers until full. Pour ⅓ cup of water on the bottom of the dish. Cover tight with foil and bake for 25 minutes.
Remove foil and bake 5-10 minutes more until peppers are soft. If using some type of cheese, sprinkle the cheese on the peppers when you remove the foil. If using nutritional yeast or Vegan Parmesan Cheese, you can just sprinkle it on right before serving.
Notes
Everyone can top their own pepper their way - like regular cheese if they aren't vegan.