On a certain Pokemon that you want to catch and it's hard to catch it with just a Poke Ball, a Great Ball, or an Ultra Ball. I don't know where else you can get Master Balls besides the Silph Co. I usually use the Masterball on legendery Pokemon.
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Mewtwo I guess????
You should use it on one of the 'roaming' pokemon, like Cresselia in Diamond/Pearl/Platinum.
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
you can use master ball in caught the groudon
no, you don't have to use your master ball on it. you could use it for any legendary Pokemon like mewtwo, or... you know what i mean!