Preheat your oven to 350°F.
Heat the oil in a large oven-proof Dutch oven or pot over medium low heat. Add the mushrooms, fennel and onions, and cook until onions are soft and mushrooms have browned.
Add the garlic and cook for about two to three minutes more. Remove from heat.
In a large bowl, add your lentils, quinoa, and mushroom mixture. To that add your herbs, fennel, and half the jar of marinara. Stir and combine well. Season to taste with salt and pepper.
In the dish you used to cook the onions and mushrooms, spread the remainder of the marinara or tomato sauce on the bottom of the dish, and add up to 1/4 cup water to thin it out a little. Fill each pepper with the lentil mixture then place into the dish. Top each pepper with a spoonful of marinara.
Return the tops to their respective peppers, cover the dish, and bake in your preheated oven for 30 minutes.
Remove the lid from the pot, remove the tops of the peppers and braise a little more sauce over the peppers. Return the pepper tops and cook for about 10-20 more minutes, uncovered, until peppers are cooked through and tender.
Remove from the oven, let cool ten minutes then serve over remaining tomato sauce.