If you completed the game and walk to elm's lab you see
That the last pokeball is gone does anyone knows where it is????
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It just disappears. There is no explanation of where it goes, but you cannot obtain it in anyway.
The last pokeball is ether with profeser elm or with lyra but lyra only takes maril so I think profeser elm has it
Proffessor Elm probably tok it to keep it safe as your rival ....... Stole the other one. I hope this answers your question.
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