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I was curious because I had a level 100 at the time I caught "The Delta Pokemon."

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it just keeps re-spawning in front of you until you catch it (you have the option of walking away, but Rayquaza will stay there). On a side note, it appears to have a modified catch rate, I caught it at half strength with a pokeball

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That explains why I caught three in a row with a Premier Ball...(I died three times to Deoxys)