Can I get any of the Regi Trio or Rayquaza if I run from them in battle? Does it effect the requirements to get them available in any way?
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In Ruby, Sapphire, and Emerald, there is no way to fight any legendary Pokémon again if you either defeat or run from them; they will disappear from the world and you will not have another chance.
For this reason it's generally advisable to save your game before fighting any legendary Pokémon. Some later generation games have included second-chance methods for legendaries, but R/S/E do not have any.