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Go to the Weather Institute near Fortree City and go to the second floor. Go to the left and talk to the professor.This depends when he says there is a drought, that's groudon, if rain, kyogre. The location also changes if you don't make on time. One tip: If you are looking for Kyogre after talking to the professor, look at the middle of the ocean and look for a small diving spot that when you go in the cave you'll find then dive again, the place you 'd supposed be is Marine Cave.
Sometime after you beat the elite 4, go into the weather institute somewhere near route 119. Then talk to the people that's in there. He'll say that there is some weather problems in some random route. Go to that route and there will be a cave opening that is not supposed to be there. If the route had rain, kyogre will be in the cave. If the route had sunlight, groudon will be in the cave. Both will be at level 70. Be prepared to buy alot of ultra balls and timer balls.
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