Meta Battle Subway PokeBase - Pokemon Q&A
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There's no right or wrong answer to this question, as all we learn is that it's gone. Common hypothesises on this topic include another trainer taking it and prof. Elm raising it himself.

But I guess we'll never know.

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Wait. Do you mean the first starter to disappear when you first start the game whom is taken by your rival or the other unrevealed starter whose pokeball is gone from the lab after you beat the game?
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Nobody knows... Seriously. It just disappears from Professor Elm's machine with no explanation, so that leaves us with nothing.

However, since it does leave the machine after some time in the game it perhaps was given to Kris, since that is the last main game character (she's from Crystal version). Or it was moved someplace else that was safer.

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