It disappears and there is no other way to meet it again.
Rayquaza is at sky pillar, to get there go to pacificlog town and go right on the sea. There will be lots o boulders there, and you will notice that there's a hole between the boulders, go through it and you will find sky pillar. Note: You can't get rayquaza unless you've defeated the Pokemon league
Go to Sootopolis.
Only in Emerald. Go to Sky Pillar
You go to sky pillar and awaken rayquaza then rayquaza will fly out of sky pillar. Then go back to the place where groudon and kyogre is. IF YOU DONT KNOW WHERE SKY PILLAR IS I SUGGEST TO GO FIND HELP ON GOOGLE, YOUTUBE.
go to puzzle in sky pillar
you go to the sky pillar and awaken rayquaza
After Groundon dissappears go to Sootopolis and find Steven, he will show you the way to Wallace. Find Wallace and he will tell you about Rayquaza. Tell him he is at Sky Pillar and then go to Sky Pillar and awaken Rayquaza.
You go to Sootopolis City. There you will see Groudon and Kyogre fighting, and Rayquaza goes to stop them. Then he goes back to the Sky Pillar.
Go to sky pillar climb to top the there it is the end
go to the top of sky pillar and you will find him
yes you do then go to sky pillar (on the right to pacificdalog) you have to have a mach bike to get up to rayquaza
sky pillar near pacifilodge city. use surf and go to sky pillar. he is at the top you penises.