You can find Rayquaza in the Sky Pillar, in the upper portion of route 131. You”ll have to go there when following the main quest when you”ll have to “wake up” it after the start of the fight between Kyogre and Groudon. You won”t be able to catch it then because it will fly away, although you can actually go back there once the fight between the other two legendaries stops and try to catch it. It will always be lv. 70.
Get some Pokemon that can battle on par with a level 70, at least one knowing the moves Sing or Hypnosis, or another sleep-inducing move.
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Fly to Pacifidlog Town.
Surf to Sky Pillar, and you must have a Mach Bike. Some of the floors have weak spots, which you can only go over if you”re going at full speed on the “Mach Bike”.
Save the game. This is extremely important, just in case you can”t catch Rayquaza the first time. Take as many Ultra Balls or Timer Balls as you can.
Get Rayquaza”s health down to low yellow or red. Then use Sing, or any other move that puts Pokemon to sleep. Keep trying with the Ultra and Timer Balls, and eventually you”ll catch it.
If you white out, run out of Poke Balls, or accidentally faint it, turn the game off since you saved it, then fight it again.
(Source) has additional pictures if needed.
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