Place the rice and 2 cups (500ml) 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 frypan 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 frypan. Rub tuna with remaining 1/4 teaspoon pepper and salt. Place tuna in the frypan and cook to desired doneness. Set aside, and keep warm.
Place shallots in frypan. Increase heat to high, and pour in 3/4 cup (190ml) 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.