Kyogre and Groudon fight when they are awoken because millions of years ago (in the Pokemon universe) Kyogre was born in a deep ocean trench, Groudon was formed underground in pools of magma, and Rayquaza was born out of minerals (like ozone) in the air. Kyogre and Groudon went on to expand the seas and land, respectively. Rayquaza however, went around to aimlessly fly in the air.
Whilst Groudon and Kyogre were expanding their domains, they met, and instantly became rivals. They fought for millions of years, expanding the seas and land and having apocalyptic battles. Suddenly Rayquaza dove out of no where, and put them both into "eternal slumber" so they would stop fighting. No one won the fight, which is why when Archie wakes them up in Emerald, they fight.
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They fight in Sootopolis City (Japanese: ルネシティRune City) (Emerald only)
kYOGRE AND GROUDON ARE IN POKEMON MOVIE UR MOTHER
It's the whole space, time thing like between groudon and kyogre.
First you need to gave caught the kyogre or groudon in heartgold or soulsilver. Then go to professor oak's lab put the kyogre first or groudon
find groudon at the magma cavren and kyogre at marinea cave