If you mean after you beat the 3rd gym leader (or was it fourth?), he runs away to get stronger. Don't worry, you'll see. When you get to victory road, he'll catch you right before you leave Victory Road, and request a battle. Good luck, cause it's one tricky fight after going all the way through Victory Road.
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go route112 after you saw team aqua run away in meteor falls and ride the ferri
If your legendary Pokemon run away in Shiny Gold, there is no way of retrieving them again.
use mean look for not leting them run away, ghost Pokemon could learn it
they run away into the wild so u can find them anywhere they run away into the wild so u can find them anywhere
use a ghost type Pokemon with scary face so it cant run away and then use a dusk ball or a net ball and you will get it don't fly or it will run away