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To obtain another Master Ball after having already used the first one, you must have some luck on your side. The Goldenrod Radio Tower has a Lottery Corner, where if all 5 numbers of the ID of any of your Pokemon match (including those in the PC), you will receive a Master Ball. You can do this multiple times, but takes a lot of luck and patience. You can also have a friend trade over a Pokemon with it holding a Master Ball. If you have an Action Replay, you could use a code to get another Master Ball.
the ultra ball is what i used to catch it...but you could use the master ball after you get it
If you don't want to waste time using other balls, yes, u should. But it is possible to nab him with another ball. Lueroi, a good Youtube video maker, caught Mewtwo with a GREAT BAll. He used his master ball on something else. If you don't want to waste your MAster ball, don't.
Either, master ball, (if you haven't used yours givin to you by professer rowan) ultra ball, or timer ball.
For Zapdos: Go through the power plant and use your master ball, If Master ball has been used then attempt to capture with Great ball or Ultra ball. For Moltres: Go to Mt. Ember and climb to the summit and Moltres will be waiting. Use your Master ball, If used try to capture with Great ball or Ultra ball. For Articuno: Go to the Sea foam caves and move the boulders through the empty holes ( Strenght HM Is needed ) Articuno is tricky to catch. Use your Master ball, If used try to capture with Great ball or Ultra ball.