PokéBase - Pokémon Q&A
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In Team Aqua's hideout (east of Lilycove), there are four balls. The top left is the Master Ball. The others are 2 Electrodes, and 1 nugget. This vid may help you on how to get to that area in the hideout.

Another way to get a Master Ball is in the Lilycove department store lottery corner. If one of your Pokemon's OT (original trainer) IDs match the 5 digit number picked in the lottery, you get a Master Ball.

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Getting Master Balls There is a Master Ball in Team Aqua's hideout just east of Lilycove city. Inside, you must use a series of teleports to get an area with 4 item balls. The top left will contain the masterball. The top right and the bottom right are wild Pokemon.

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