PokéBase - Pokémon Q&A
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Honestly, there's really 5 Pokemon you should use it on.

  • Mewtwo: His low catch rate is just annoying, and he has moves that can stall you out due to their rather high PP (Guard Swap, etc)
  • Latias: Its roaming, so to stop it from doing so, use the Master Ball once and for all.
  • Lugia: It's really annoying due to its high bulk, but is managable with Ultra Balls.
  • Entei, Raikou: Same reason as Latias.
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Depends on what you want to catch that is extremely hard to catch. It's your choice but do not use it on something foolish like the three legendary dogs. That is a bad idea. I would ither go for Lugia of Ho-Oh since you play Heartgold and I play Soulsilver lol but I would recommend Lugia for hg and Ho-Oh for ss. Hope I helped. Or.....Mewtwo. That is very hard to catch but might be achievable with dusk balls but you have to do some pretty good stat changes to it.

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You could either save it for a Pokemon you really want that might escape, like a shiny. Or you could use it to get a rarer Pokemon like Ho-Oh, Lugia, one of the three roaming dogs, or any of the other legendary Pokemon in the game.

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Use it on roaming Pokemon (Entei, Raikou or Eon Duo). It guarantees capture and you don't have to go through the hassle of getting a Pokemon with Mean Look/Block, etc. and battling it.

Either that, or use it on Mewtwo, since nobody likes a capture rate of 3.

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