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Defeating Kyogre in Pokémon Sapphire and Pokémon Emerald will mean that it will not return however it will return if you defeated it in Pokémon HeartGold. In Pokémon HeartGold, there's a regeneration system that will regenerate all 1-off Pokémon such as Kyogre, Entei, Suicune and Raikou after defeating Lance.

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Q: What happens if you defeat kyogre?
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