Finding the Gelnika (The "Sunken Plane")
WARNING: This page contains SPOILERS for Final Fantasy VII.
Take the sub (from the Junon dock) almost due west towards the Gold Saucer. There is another sub dock right there. Face the Saucer and turn left. Float towards the land until you are very close to touching it. There should be land to your left, right, and directly in front of you. Submerge the sub and look around carefully (Emerald Weapon can sometimes sit right by the Gelnika). See the gray wreckage that looks like an aircraft? That is the Gelnika. Drive the sub directly into the Gelnika once you are sure Emerald is not around. Your party will automatically enter the plane.
The Gelnika is fairly easy to navigate. There are three items that might elude you though:
Yuffie's Conformer: From the entrance, take the door that heads up above the save point. Check the upper-left corner of the lower level to find the Conformer.
Double Cut Materia: From the entrance, take the door that heads up above the save point. Check the upper-right corner of the lower level to find the Double Cut materia.
Hades Materia: From the entrance, take the door that heads left. Exit this vertical hallway. Go to the bottom level of this room. There is a wrecked helicopter inside this cargo bay. Hades is in the rubble of this helicopter. If you stand still, you should be able to see the materia flash every few seconds.