Note: The Emerald WEAPON may be outside the Gelnika if you have not fought it yet. You may choose to engage it in battle by approaching it. If not, exit to the surface and re-enter the water and it should be gone.
Approach the Gelnika with the submarine and you will be able to enter the plane. In the first door on the top of the screen, you can find several items including Yuffie's ultimate weapon, Conformer. Exit this room and continue on. When you enter the hallway to the left, if you haven't already fought the Turks during the mission to stop the Sister Ray, your party will run into Reno and Rude and enter into a battle. After the battle, enter the cargo bay to find some useful items including Cid's 4th Limit Break, Highwind, and the Hades Materia.
Note: If you enter into a battle with a Ghost Ship, Morph it to receive a Guidebook, which is used in the side quest "Kalm Traveler"
Note: If you haven't fought Emerald WEAPON, save your game before exiting the Gelnika. Emerald WEAPON may be outside and you will automatically engage it when you exit the sunken plane.