To get to Rayquaza,you have to progress far enough in the game.After you beat Groudon in magma cavern,Xatu will summon everybody at the Grand Canyon and will say a meteor strike earth.He will tell you to get help from Rayquaza at the Sky Tower.There are some pretty strong pokemon at the Sky Tower,so don't leave for the Sky Tower yet,you should train first,when you think you are at a high enough levelthen go,remember to bring a lot of reviver seeds and heal items because Rayquaza is really strong.I recommend that you be level:60 or higher.There are 25 floors at the Sky Tower.After you clear 25 floors,you will reach a stone,you can save there.Rayquaza is on the 9th floor of the Sky Tower summit.Prepare for the fight of your life,its a tough battle.