Where do you get the master ball?
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Professor Krane will call you and ask you to come back to the lab at a certain point in the game, he then takes you down a secret staircase and gives you the Master Ball.
Well somewhere near the end of the adventure, go to the HQ Lab and talk to Prof. Krane and you and him will walk to a secret base that there's a chest with the Masterball in it.
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