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After you beat the elite 4 and get the national pokedex, go to prof oak in pallet and he will give you a Kanto starter. Then Mr. Pokemon will give you an orb (Red in SS and Blue in HG). If you take that orb to the Embedded tower, south of safari zone, you will fight one of the R/S mascots (red - Groudon, Blue - Kyogre) If you catch it, then import the other one from the opposite game you can take them to Mr. Pokemon (MUST be a Groudon caught in SS and a Kyogre caught in HG to work) and he will give you the jade orb. take the jade orb to the embedded tower to fight/catch rayquaza.

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