it's escaping me right now as to which orb you get in which game. you either go to mr pokemons after giving him the red scale and battleing red. or as the case may be, you have to buy ss and get it then.
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After you beat the champion, go to Mr. Pokemon and he will give you either a Red Orb or a Blue Orb depending on which game you have. Also, when you get both Groudon and Kyogre on one HG or SS, you can get Rayquaza.
U only get it in HG
You need to show Prof. Oak a HG Kyogre and a SS Groudon from the Embedded Tower to get the green orb.
You aren't supposed to get the Blue Orb in SS, only in HG (You don't get both Kyogre and Groudon).
the red orb gives you the chance to catch groudon and the blue orb gives you the chance to catch kyorge.