Place the rice and 2 cups water in a pot, and bring to a boil. Cover, reduce heat to low, and simmer 45 minutes.

Heat 1 tablespoon olive oil in a skillet over medium heat. Stir in onion, and cook until tender. Season with thyme and 1/4 teaspoon pepper. Gently stir into the cooked rice.

Place the edamame in separate pot with enough water to cover, and bring to a boil. Cook 5 minutes, or until tender. Mix into the rice.

Heat remaining olive oil in a skillet. Rub tuna with remaining 1/4 teaspoon pepper and salt. Place tuna in the skillet, and cook to desired doneness. Set aside, and keep warm.

Place shallots in skillet. Increase heat to high, and pour in 3/4 cup water. Cook until liquid is reduced to about 1/2 cup, then stir in chives, orange zest and orange juice. Arrange fish over the rice and drizzle with the sauce to serve.