I fainted groudon. What happened next?
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The goal is actually to catch Groudon. Since you made it faint, you will have to defeat the Elite Four again in order to find Groudon back in the Embedded Tower.
After you catch Groudon, you will have to trade for a Kyogre that was found in the Embedded Tower in order to have the chance to battle/catch Rayquaza. Once you trade for a Kyogre, show it and Groudon to Professor Oak. He will give you the Jade Orb. The Jade Orb allows you to find Rayquaza in the Embedded Tower.
Hope this helps!
Don't use your master ball. I caught Lugia with one ultra ball. Fainted groudon got confused and reset, lol. Use your master ball to catch a shiny or something. All legendaries can be caught with ultra balls - figured that out with moltres.
-Katie Ann
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