You get the Master Ball in the Aqua base off of Lilycove. It is in an area with two Electrodes and one Gold Nugget.
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team aqua hideout at lilycove city
To catch Kyoger with out a master ball weeken him a liltel bit or paralize confuse burn or freeze him and use net and dive balls.NEVER WASTE A MASTER BALL ON KYOGER!
back in your house you can only get it in the first hour of playing
there are 2 master ball s and a master ball is rare you can only use it for kyogre requaza groudon salmence fly gon and the rest of the strongest Pokemon a master ball always captures a Pokemon no Pokemon can break out its in possible
its in the team aqua/team magma (for ruby) hideout near lilycove. the first two are electrode and the second two(the ones near the wall) is a master ball and a nugget.