Pick over and rinse the lentils, then place in a pot with 3 cups of vegetable broth. Bring to a boil, then reduce heat to medium low and cook until lentils are tender, about 30-35 minutes. Add more broth if the lentils start to dry out.
While the lentils and the rice are cooking, cook the onions. Place the onions and two tablespoons olive oil in a large skillet and cook over medium high heat. Stir often, and if they start to brown too quickly, reduce heat to medium. Cook until the onions are all browned and some of them are crisp. This could take about 40 minutes.
Once everything is cooked, add the rice and lentils to the onion skillet. Season with the sea salt, pepper, and nutmeg. Stir well and serve right away.