You take it to the researcher in the bridge of the abandoned ship, and he will then tell you to take it Captain Stern in Slateport City (At the ferry depot). Stern will then offer you a Deepseatooth or Deepseascale which you can use to evolve a Clamperl into a Huntail or Gorybess, respectively (I would recommend Gorybess, good special attack and access to ice beam and psychic, and maybe hidden power electric).
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you get the scanner on the abandoned ship.
actually the scanner is ina pokeball in rm 2........
there is no scanner on fire red/leaf green. Only on ruby, sapphire, emerald
The scanner can be found in the abondand ship on route 108 in Room 2... but first you must have a Pokemon that can use the dive hidden machine and you must find the room keys to the other rooms that are lying in the rooms. Its is an easy process
its not an emerald its RAYQUAZA the main legendary Pokemon in Pokemon emerald.