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with the raquaza person...you should have saved the game before hand.
I havent actually spent time looking for shinies...but I have come across a red gyarados(hehe, I know, i know) no I have actually come across a red gyarados by accident while fishing. Ive also bumped into a shiny sandshrew while walking through Union Cave(in jhoto) and a shiny abra by trading in coins at game corner(the odds of that happening...hey odds...game corner...hehehe)
mmm, even if you saved the game before fighting rayquaza, if it were shiny and you fainted it, then reseted, it wouldnt be shiny again so taht kind of... innecesary to say, its obvious that the "rayquaza guy"saved the game befor fighting rayquaza