Alrighty, let's get down to business. Go to Junon. (You know where that is.) Go left of the elevator, which you have to pay the guard 10 gil. (Does he think I'm made of money?!) Keep heading down the path until you see the dock where Rufus and Heidegger decended with that pretty ship first time you arrive. Go one screen left and you'll see the passage to the Underwater Reactor.

Once there, proceed until you cross that freaky elevator where you see the bubbles rise up as it goes down. One screen from there and you'll see a glass tube hallway with some freaky fish swimming around. Run randomly until you see the Ghost Ship. (The huge one with that creepy "Knockout" attack) Whittle it down until it has next to nothing in HP, then use that Morph materia you got from the Ancient Temple and you'll recieve a Guide Book.

Get yer ass to Kalm to trade your Guide Book for your precious Underwater Materia. Now you can decend into the waters near Junon and confront your Emerald Weapon. (How your BEAT him, I cannot say. Gameshark works wonders, but true pride is lost.)