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Heat 1 tablespoon of the oil in a Dutch oven or similar large, sturdy-bottomed pot over medium heat. Add the onion and cook for 5 minutes, or until the onion is beginning to soften, stirring occasionally. Add the Italian seasoning, ½ teaspoon kosher salt, red pepper flakes, and garlic. Let cook just until the garlic is fragrant, about 30 seconds.
Add the lentils, quinoa, broth, fire-roasted tomatoes, and sun-dried tomatoes. Bring the mixture to a boil, then reduce heat to low. Cover and simmer for 25 to 28 minutes, or until the lentils are tender. Stir once halfway through, then again towards the end of the cooking time. If the mixture looks too dry, splash in additional broth or water. Stir in the nutritional yeast.
While the lentils and quinoa cook, preheat your oven to 400 degrees F. Lightly coat a 9x13-inch baking dish with nonstick spray. Slice the bell peppers in half from top to bottom (I cut right down through the stems). Remove the seeds and membranes then arrange cut side up in the prepared baking dish. Drizzle the insides with the remaining 1 tablespoon oil and sprinkle lightly with salt. Carefully pour a thin layer of water into the bottom of the pan. Place in the oven and bake, uncovered, for 20 minutes. This step gives the peppers a head start while the filling finishes up.
Carefully mound the cooked filling inside of the peppers. If using a non-dairy “mozzarella” sprinkle it on top. Return the pan to the oven and bake for 5 to 10 additional minutes, until the peppers are completely tender and the filling is piping hot. Sprinkle with fresh basil and enjoy!