if you want to catch them you go back to fortress city, go to weather institute and from there go upstairs all the way to the left (must beat eliete four first) talk to the scientist (there is only 1) and from there talk to him he will say it's raining/very sunny on Rotue something go there and you'll notice it wasn't like that before (make sure you have Pokemon that knows dive) look for a dive spot that wasn't there before go in there go in the cave and boom Kyogre awaits you, for groudon same thing go to route whatever and it'll be really sunny look for cave that wasn't there before da-da!
P.S Don't use Master balls, use it on 1 of the Regis or a shiny Pokemon
sootopolis city
You have to catch Kyogre and Groudon.
if you mean between kyogre and groudon, then the battle in sootopolis.
Sootopolis City
In Pokemon Ruby and Sapphire there is no battle between Kyogre and Groudon. That is only in Emerald version. Instead the legendary pokemon (in your case Groudon) is inside the cave of origin in Sootopolis City.
You can't get Kyogre in Pokemon Ruby but you can get Kyogre in Pokemon emerald and sapphire and in ruby you only get groudon and rayquaza. In sapphire you get Kyogre and rayquaza and in emerald you can get groudon, Kyogre, and Rayquaza.
you get it at cave of origin but you have to beat the gym leader of sootopolis city to use it on the waterfall to ever grande city
groudon,kyogre,rayquaza
You don't
They fight in Sootopolis City (Japanese: ルネシティRune City) (Emerald only)
Wallace gives it to you you in sootopolis city when groudon and kyogre are on a rampage
In Pokemon Emerald, Groundon and Kyogre are legendary Pokemon. You can find them in the Marine Cave and the Terra Cave.