All legendary pokémon can be caught with Ultra Balls, but your team needs to be strong in order to get them weak enough for a decent capture rate. Because the birds (Articuno, Zapdos, Moltres) and Mewtwo sit in one place, you can save before the fight and keep trying until you get it right.
That being the case, I would use the Master Ball on the roaming pokémon (Suicune, Entei, or Raikou) that appears after the elite four has been beaten. These three legendaries travel around the map quickly and will flee from battle, making them rather time-consuming to hunt. Instead of preparing a team to nab it, simply using the Master Ball when it shows up will guarantee a capture and save a lot of time in the long run. Remember that only one of the three will show up in your game. Which one it is depends on which pokémon you started with: Entei if you picked Bulbasaur, Suicune if you picked Charmander, or Raikou if you picked Squirtle.
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You can't. You can only get one Master Ball.
The master ball code is: 82003884 0001
you will only be given one master ball.
You could use any ball but I suggest weakening them to 1 HP first, then putting them to sleep, then catching them with an Ultra Ball. DON'T WASTE YOUR MASTER BALL ON THEM!
weaken it's health to red and paralyze it. use tons of pokeballs or other kinds.