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My problem is that my sapphire and ruby there internal battery has run dry. I just want to find out if I would be able to still get a master ball in the game like normal. Also where do I find them?

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Yes. You'll be able to find it in a room at the Magma or Aqua Hideout after Mt. Pyre.

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Yeah, I missed that one because usually, you get the master ball after the E4.
I seriously missed that one.
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It is in a room in the Magma/Aqua hideout. You need to teleport using the portals on the floor to get there. Watch out, it is near Electrode.

This video will help.

http://www.youtube.com/watch?v=jGTJRi-yZQI

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