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To get Rayquaza, you have to obtain the Blue Orb from Mr Pokemon, and catch a Kyogre on Route 47. Then you need a friend with Soul Silver to get the Red Orb from Mr Pokemon, and catch a Groudon on Route 47. Your friend needs to trade the Groudon to you, then you need to show both Kyogre and Groudon to Professor Oak. He will give you the Jade Orb. Go back to the Embedded Tower on Route 47, and Rayquaza will be there

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