Well, there are ALOT (and when I say alot, I mean ALOT? of very strong Pokemon in Emerald version. Keep in mind it is, like, Ruby and Sapphire COMBINEd into one. But the strongest Pokemon to ever meet or encounter in Emerald (because I think it can be found only in emerald.... maybe fire red) Would probably be the ULTIMATE Pokemon............. Mewthree X! It might be only available through cheating with action replay, but i have absolutely no clue what the action replay code is,... I.. I don't HAVE an action replay use Google to find it or something.
Mayby Rayquayza
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Groudon or Rayquaza is the strongest Pokemon in Emerald. Groudon isn't as legendary as Rayquaza, but it lacks Sp. Attack. but suffices in Attack. Metagross or Deoxys would be third strongest.