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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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Q: Why does Groudon and kyogre fight?
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