Pre-heat the oven to 400 degrees. Grease a 9 x 13 inch pan.
Over Medium High heat, add water and rice to a large saucepan and bring to a boil. Once boiling, reduce heat to low and cook rice for 40-45 minutes.
Meanwhile, prepare the Cheese Sauce. In a medium saucepan, over medium-high heat, cook the onions in the butter until tender and translucent. Mix in the flour to form a paste. Pour in half of the milk and whisk until well combined with a wire whisk.
Add the rest of the milk and continue to stir until the mixture begins to bubble. At this point, remove from the heat and add the shredded cheese. Stir until the cheese is completely melted. Season with salt and pepper. Set Aside.
Add all vegetables to a large, non-stick skillet. Over medium-high heat, cook the vegetables with a dash of water and cover with a lid. Mix occasionally to prevent scorching.
Add cooked rice, chicken, and cheese sauce to the vegetable skillet, and stir to combine. Pour the rice mixture into the greased pan, and top with shredded cheese.
Bake for 15 minutes until warmed through and the top is crispy.