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To catch Raquaza you have to get Groudon and Kyogre in the same game (Groudon Lv. 50 soulsilver, Kyogre Lv. 50 heartgold).
If your playing Soul Silver, catch Groudon. If playing Heart Gold, catch Kyogre. Trade Kyogre or Groudon to either game. They both HAVE to be from Heart Gold or Soul Silver. Then cannot be migrated from Sapphire, Ruby, or Emerald. Then visit Professor Oak while having Kyogre and Groudon in your party. Show them to him and he will give you the Jade Orb (I think it should be called the Emerald Orb). Then go to Cianwood. Go inside the Embedded Tower and Rayquaza will be there.
To get Rayquaza you must have gotten Groudon from Soul Silver, and must have gotten Kyogre from Heart Gold. It has to be those Pokemon from those games! It CANNOT be from GBA games.

First, Capture Groudon and Kyogre.

Next, Talk to professer Oak, and he will give you the Jade Orb

After that go to the Embedded Tower (Place where you got Gorudon)

He will be there at Level 50!

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