Preheat oven to 400 F, and spray a 9x12-inch baking dish with cooking spray.
Cook the rice according to package instructions, using the stove or a rice cooker.
Add the oil to a large skillet, and once it is warm, add in the onion, garlic, red pepper, green pepper, and jalapeño. Cook for about 5 to 8 minutes on medium-high heat.
Add in the black beans, pinto beans, corn, fire roasted tomatoes, green chilis, lime juice, and spices. Stir to combine.
When the rice is finished cooking, add it to the skillet, and stir well.
Add the mixture to the baking dish, and top with the cheese. Bake in oven for about 10 minutes.
When the casserole is done, add toppings and serve.