Of course you can. An easy way to do this is get a Pokemon that knows the moves Hypnosis or Spore, and put the desired Pokemon to sleep. Next, whittle away at its HP with not-very-effective moves. Take a long time, so the ever-handy Timer Ball can come into effect. Then use any of the following Pokeballs. I have listed them in preferable order: Ultra Dusk, (if in cave or night time) Timer ( in obvious circumstances) Heal Net (if the type is desirable) Great Poke
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Of course, a Master Ball catches any Pokemon without fail, Legendary or not.
You can't catch shiny legendary Pokemon without cheats... sorry
you have to get more then 45 gym to catch legendary Pokemon! deoxys is a legendary Pokemon
defeat all gyms,elite 4 and champion of that region to catch legendary pokemon
The Master Ball isn't a necessity, since any Pokemon can be caught without it. Use it when you have spent around three days (a couple hours a day) trying to catch a rare Pokemon (legendary only) with Ultra Balls at low HP and with a status problem. It is wise to do so, since you may find that a Pokemon may be tough to catch and you might not have your Master Ball.