Well, mabye you haven't checked all the places. After you find him in the burnt tower it should be north of Cianwood City which I'm guessing you check already, then it should be outside the entrance of Mt. Mortar which you probably checked then it will leave Johto and be a Vermillion City and then it will be in Route 14 where it escapes for the final time and you see it outside of Bill's House in Route 25. If you have checked everywhere I have mentioned then you should look up a video! Hope I helped!