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Go to the Cave of Origin in Sootopolis, and talk to Wallace, tell him you think Rayquaza is in the Sky Pillar. Then you have to release Rayquaza (Route 131, Sky Pillar) and then fly back to Sootopolis, and Rayquaza will quell the fighting, and then Kyogre, Groudon, and Rayquaza will disappear. You can now fight Juan. Rayquaza will now be able to be caught in the Sky Pillar, you can't get Kyogre or Groudon until after you fight the Elite Four. Go back to the Weather Institute and talk to the guy on the second floor, first he will tell you where heat waves are occuring, go there and catch Groudon. Go back to the Weather Institute and talk to the guy on the second floor again, and he will tell you where downpours are occuring, go there and catch Kyogre. Yay, you caught three of the legendaries! :D

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