PokéBase - Pokémon Q&A
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You go to Mr. Pokemon after beating Red on Mt. Silver and he will give you a red orb. You then take that red orb to the embedded tower which is near the safari zone in a place where you need rock climb and surf to get to. You will then see a hiker standing next to a cave door and inside should be Groudon if you have collected the red orb already. If you are playing HeartGold you would've got the blue orb for Kyogre instead. You need both Kyogre and Groudon in either game to get the green orb from Prof. oak to find Rayquaza. Hope I helped.

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You need to obtain the red orb from Mr.Pokemon. He gives it to you once you have access to the National Dex, and have recieved the Kanto Starters from Prof. Oak. Then you need to head to a cave in Route 47, the Embedded Tower.

Source: http://serebii.net/heartgoldsoulsilver/legends.shtml

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You'll also need rock climb