you have to get to the cave somehow,then after everything is done,goto the skypillar
somehow.the solve the puzzle needed to get to the rooftop,fight rayquaza and finish it off
then fly to sootopolis again after a little while you will see Rayquaza emitting something
and then the 3 ancient pokemon will go away after that surf to the gym and talk to Maxie
and Archie,they will dissapear then talk to wallace then you should know what to do