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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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What happens after catching Kyogre?
you have a new Kyogre and become epic, congratulations!
What do you do after you defeat the 6th gym leader in Pokemon Sapphire?
Go on to defeat the seventh gym in Mossdeep City, if you did not already catch Kyogre.
What happens if you made the Kyogre faint in Heartgold and saved it?
It will come and kill you in your sleep. Goodnight
In heart gold if you killed Kyogre where can you find him again?
Go defeat the elite four again and all non caught legendary Pokemon reset
How do you get the Wailmer to move from Lilycove City?
You'll have to go into the cave that is just north of them and defeat team Magma/Aqua. Then you might have to fight Groudon/Kyogre. After that they should have moved.
