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Groudon = Land Cave
Kyogre = Undersea Cav
After waking up Raquaza and having him stop their war, the weather institute (all the way north of Route 119, to the left of Fortree City) will report abnormal weather patterns on various routes. Go to those areas and enter either a hole in the wall or a dark patch of water (using dive) and you'll find a cave where Groudon or Kyogre can be fought, respectively. Raquaza can be found on Sky Pillar (route 131, east of pacificlodge town).

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Q: Where are the legendary Pokémon on Pokémon emerald?
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