You will see Tornadus again. It is a roaming Legendary, meaning it changes Routes after you encounter it / change Routes. Check the signs in the house thingy between a Route and a City. They will say a storm is occurring. Don't go to that Route, Fly to somewhere around it.
>Wherever these Pokémon appear will be subject to weather identified as "stormy" by the bulletin boards in gates. Only these two Pokémon can cause stormy weather (which is effectively rain in-battle), so they can be tracked down using the bulletin boards. However, bulletin boards are somewhat inferior to the tracking methods of previous generations, as Tornadus or Thundurus's location changes when the player exits the gate.