they are enemy since the beginning. haha XD sunlight and rain they cant get along well
if you mean between kyogre and groudon, then the battle in sootopolis.
There are many legendary Pokemon in emerald, such as groudon, rayquaza, groudon, deoxys, and such. Groudon and Kyogre are not available until after beating Wallace, but Rayquaza can be caught right after the major battle between groudon and kyogre.
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.
Better is pokemon emerald.you can catch more pokemon-you can catch kyogre and groudon-you can battle with the frontier brains and collect the seven symbols in battle frontier
You battle Kyogre for your chance to capture it in Pokemon Alpha Sapphire after you capture the groudon.
rayquaza would then groudon then kyogue
Kyogre because Kyogre is Water and Groudon is ground, which is weak to water.
First you try to get groudon and kyogre into battle, when the Pokemon league champion asks you where is rayquazza is, you say it is in sky tower.
In a battle Groudon,would win you see groudon has 150 attack and 140 defense kyogre has 90 attack and 90 defense threfore groudon rules!
Well,actually I think that Pkemon Emerald is the best,because you can catch both Groudon and Kyogre(this is 100% true) and there is a Battle Frontier.
You can go to the battle frontier, catch groudon and kyogre, and go to the secret place in the safari zone where you can catch Pokemon from the johto region.
As Wallace is the Champion of the Pokemon League in Emerald, you must first: Visit the Sky Pillar and tame Groudon/Kyogre Defeat all 8 Gym Leaders Defeat the Elite 4