In ruby/sapphire go to a place called the sky pillar after you beat the E4 you need a Match Bike to do this in Emerald you go to the Sky Pillar as it is part of the story' line you need the Match Bike too it is at LV 70 so be ware
well you have to beat the elite four first and then surf east of pacifidlog town to sky pillar where you will need the mach bike to cross the cracks in the floor and rayquaza will be at the top of the pillar.
Sky pillar, Its north-east of pacifilog, I suggest taking some repels and some good pokemon, You will also need a macth bike due to the breaking floor, Rayquaza is located at the very top of the pillar.
I THINK in emerald,i dont have to beat the E4 for rayquaza,and ruby,saphire,u have 2
Mach bike is for the cracks in the floor and only passable on the bike
it wont let me in the plce rayquaza is at i got to skypillar the front entrance walked in then walked out the other exit and there is another building and it says the door is closed???
just like everyone said - in R/S you have to beat the elite 4 1st- in emerald an easier way to think of it is just get all 8 badges THEN go to Sky Pillar and then the door should be open and there should be cracks in the ground you need to overcome.