of course you should itll get him in 1,2,3
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you should use it on a very hard legendary Pokemon like dialga palkia giratina shaymin or arceus
When you come to meet Palkia or Dialga at MT.Corenet
you should use your master ball on anything that's rare (not like a shiny) you could use it on lugia, or you could just use hypnosis or somethin then use some ultra balls. if u have the arceus from the movie, do the event and use the master ball on either dialga, palkia, or giratina ( depends on what you choose)
Use Kygore in the cave of origins you don't even have to attack! Walk up to him the orb should be glowing and then the battle, use the master ball and done! 1 Kygore! But there's one on master ball in the entire game! So use it here.
Its always too hard to catch. But you can use a Master Ball right away or a Quick Ball. Occasionally, if its weakened, you can throw a lucky Poke ball at it. That's how I got my Dialga!