Go to the soldier at the north of the town and pay him to ride the elevator. Press the panel to ride it. Go to the main road in Junon and go south then north until you reach a grey corridor with an officer drilling his men (he’ll be blowing a whistle). Go towards them and follow them through the door to the left. In the elevator, you’ll fight some soldiers. At the bottom of the elevator you have to fight some more soldiers. After they’re done, go south then left. Then go right down the stairs and save. Go down the next elevator. Go north through the underwater tunnel. Go into the chamber at the end and press the red switch. Then go back out the door you came from. Go along the walkway past some submarines, and hit a Save Point in the next hall. You can talk to the guard in the north and he will fight you, then two more soldiers will; if you don’t talk to him all three will fight you. Got to the right and fight more guards. Make your way across the walkway and see the Huge Materia being loaded. Keep going right and you’ll meet Reno of the Turks again, but he will sent a metal machine after you instead…
If you have Knights of the Round, this boss can be killed in one go. Otherwise: All three parts of this boss are weak against Lightening, so use Ramuh and Bolt as much as you can. The guy’s arms can imprison one or two of your allies, and they receive a third of the damage the boss takes, so if they are caught try not to use anything that hits more than once. The only way to get your allies back during the battle is to kill off the arm they are held in, or to have that character die. Once you have your characters back, use Phoenix to restore them and hurt the boss. This guy has a pretty nasty attack called Lapis Laser which can take off about 1,500 HP so watch out for that. You’ll get the God’s Hand once you’re done.
Head to the left to get the Battle Trumpet. Then head towards the guards in the background. Get the Scimitar from the chest by the stairs and the Leviathan Scales in the chest to the left. Then go up the stairs and fight the guards. Cloud will then get in the sub and you’ll have to fight the three guards in here. Save after killing them, then go to the door to the north to meet the commander and two soldiers. You can either choose to let them live (bottom option) or fight them (top). Afterwards examine the chair and read the manual then sit in the chair. Then pick the bottom option to start a mini game:
Use square to shoot torpedoes when near an enemy sub. X Speed Down, Triangle Speed Up. Most is explained in the manual. You have 10 minutes to complete the mini game. First locate the red Shinra sub and continually shoot torpedoes at it, you can also destroy the yellow subs too. Watch out for mines, and if WARNING comes up an enemy sub is approaching, ALERT when it is firing, MINE if you’ve run into a mine, and CONFLICT if you are hitting the ocean floor. When you are done, Misson Complete will appear and you can now use the sub on the World Map. If you didn’t do it, your party will jettison the sub. You will then be at the dock near Junon. Before going into Junon, get back in the sub.