Team aquas base where they first hide the submarine. It's in one of the rooms
you can get a master ball by winning the lottery in lilycove
In the Aqua Hideout.
Right of Lilicove
you can if you have a Master Ball
In lotto
die
You get the Master Ball in the Aqua base off of Lilycove. It is in an area with two Electrodes and one Gold Nugget.
In the office of team Aqua's hideout.
throw a master ball
It's hidden in Team Aqua's hideout.
Master balls cannot be bought in any Pokemon game.
Somewhere in the aqua hideout (you have to be in lilycove city)