In an 8-inch skillet, heat olive oil over medium-low heat. Add minced onion and cook until soft and fragrant, 6 to 7 minutes. Stir in tomatoes, chipotle powder, and salt, then cook until warm, 1 to 2 minutes.
Next, add brown rice and cilantro, cooking for an additional 2 minutes. Create a well in the center of the mixture and crack in both eggs. Reduce the heat to low, cover, and let cook until the egg whites are set and the yolk is at desired consistency, roughly 6 to 7 minutes for over-easy and 10 to 11 for over-hard. Serve with a sprinkle of cilantro.