I believe you meant MISSION 5. If you had caught it after Barlow contacted you in the room where the shark is, then you should have recovered it and resurface to Pueltown. Unless maybe you missed doing certain things or maybe even caught the wrong shark. The shark to catch is in the far end of the underwater area with water current. Anyway, in most cases with these Pokémon games, not being able to proceed usually means you missed doing something or hadn't talked to certain key NPC. Just back track and see if all been done.
I was contacted by barlow.. everything i needed to do, i did.. Could it be possible that it doesn't work because of it being a rom and not a original card?