If you have already beaten the elite four and have Latios or Latias already roming around in emerald then you can chase it down till you are in the same vicinity as it and go into the grass to see it appear. toss a master ball at it and you will have the latios or latias. Of course it's best that you clone the master ball first so that you can catch the other one the same way.
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Trade from Sapphire/Emerald.
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then it's gone forever