When To Use Master Ball

Back in Pokemon Red, the only wise choice to use your one and only Master Ball on was Mewtwo. It was the strongest Pokemon found in the Wild, so it only made sense to use a Poke Ball that would guarantee its capture. In Pokemon FireRed, the decision on which Pokemon to use your Master Ball on is a little more difficult. Not only is Mewtwo still found in the game and at Level 70, but Lugia and Ho-Oh can also be found (via Event or Cheat Code). Believe it or not, they too will be encountered at Level 70, making all three of these Legendary Pokemon tied for the strongest Wild Pokemon. Because of this, all three are good options for your Master Ball.

In additional to Mewtwo, Lugia and Ho-Oh all being viable options to use your Master Ball on, you can't argue with using your Master Ball on Raikou or Entei (depending on if they will roam Kanto due to your Starter Pokemon Selection) either. Both of these Pokemon are incredibly difficult to find since they will be found roaming the entire Kanto Region, but they each will try to flee from battle when found. And unlike Suicune, a known glitch basically prevents them from doing so with the Pokemon Move known as Block.