After the Weapons are released from the Planet and you have the Submarine, you will see a monster swimming around the ocean between Junon and Costa del Sol (Sometimes seen floating above the Gelnika).
This is Emerald Weapon, an optional boss fight added to the North American and European releases of the game.
As this boss is underwater, there is a time limit of 20 minutes to defeat it unless you get and equip the Underwater Materia.
There are a few things to prepare before facing this boss, below is a list of what I recommend.