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Once you have Kyrogre (in HeartGold version by getting the blue orb) and you have traded for a Groudon (in soul silver by getting the red orb), once you have both in your party, take them to Mr. Pokemon and he'll give you a Jade Orb. Take it to Embedded Tower and Rayquaza will appear.

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How do you catch Groudon on Pokemon HeartGold?

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