to get to sky pillar fly to mossdeep city then surf all the way down(the same way you took to get to sootopolis but go down even farther until you reach route 129 then go all the way left until you see a break in the rocks.go into the break and there should be a cave.go into it and you'll be at the sky pillar.
the sky pillar is full of pokemon but they are only like level 36-39.
when you reach the top,go towards rayquaza and he'll wake up and take off.
fly to sootopolis and you'll see a cutscene of him stopping the fight.
when he leaves everything will be back to normal but you can head back to sky pillar and you can challenge him.
WARNING:he will be at Lv:70 so i suggest you bring your strongest pokemon.if you want you can use the masterball on him.
oh and please don't double post.
To all of those poor unlucky souls out there, this is for you:
If you don't watch Black Cat then Train Heartnet has a message for you:
I came to deliver some bad luck.