This is how it works.
Fly to pacifidlog town. use surf on the right side of the town keep surfin but you have to be on the upper side of the stone walls, then surf past the two trainers.
Then you will see another way you can surf surf upp then you will see a cave enter the cave then get out of the cave on the other side then you will see a sky tower.
Enter it, use max repel if you have any then get on your mach bike then get to maximum speed and manuver around the cracked floors until you reach RAYQUAZA.
Save your game in front of him incase he destroys all your pokemon or your pokemon destroy him, battle him.
You must have 40 timer balls and 60 ultra balls use as many ultra balls as you can but if you dont catch him then it is timer ball in action and then BINGO you have got the strongest pokemon ever.
PS: You must have beaten the pokemon league.