The Underwater Reactor at Junon is next, so suit some people up and head out. It costs just 10 gil to hitch a ride on the elevator, so ride it up, then when you're on the streets of Junon, follow the bottom of the screen to reach the path to the reactor. The rest of the way is easy to find, and the underwater part is really cool, visually. You'll probably meet an enemy called Ghost Ship in the Underwater Tunnel--take note of him, as he's key to one of the optional quests. Eventually, you will be forced to fight another boss, and this one's really nasty. He can grab your people and disable them! The best way to beat him is to use speed. Have everyone cast their most powerful summons as quick as possible. Lightning, Kjata, Neo Bahamut, and any other mass kill spells you have are very effective.
As you approach the submarine, definitely stop and grab all the treasure. If you immpediatly go left after the boss, you get a War Trumpet for Cait Sith. Right next to the silver submarine are the first first triple-AP weapon, Cid's Scimitar, and the Leviathan Scales, a Key Item that seems to have no use unless you think about it . . . where did you get the Leviathan materia? And wasn't there some areas blocked by fire near there that you couldn't reach? Hmmm . . At any rate, kill off the Shinras, then hop into the sub. When you reach the cockpit, choose to fight the crew, because they say some funny things during the battle, and you receive a Shinra Beta for your troubles. Not great armor, but it's one of the rarer items.
This submarine mini-game is very simple, but one little screw-up will render the mission a complete failure. Read the manual very carefully, and when the game starts, follow right behind the Red Sub and fire constantly. If you draw a good bead on him and keep firing at him, you should be able to win the game very quickly. Ignore the other subs--just concentrate on the red one and never lose him on the screen. When you win, you'll receive the sub, and you can explore the underwater areas now. Don't forget to grab the Huge Materia from the sub you took out, which is just to the south of Junon, underwater, and hidden a little around a corner. It's around the area where all the seaweed is on the sea floor. There are some other things of interest down here, which are explained in more detail later. Also, you can head back to Wutai and use those Leviathan Scales in the firey cave up on those Dachao Statues. Remember that place? When you approach the fire, the scales will make it go away, allowing you to get Yuffie's Oritsuru and the Steal as Well materia. You can also, if you like, head back into Junon, but all you'll discover is that you missed Rufus.