We tackle our first real challenge...the Nepto Shrine...
The DarkFaces are easy to take down if you have Level 1 spells. Since you're shrunk down, they'll be about as hard as all the other enemies you've faced so far.
This area is very straightforward. When you're out of the hidden area, enter the cave to the north (stay Mini!) to enter the Viking Base.
Talk to the pirates. You'll find out a sea dragon destroyed their ships after an earthquake. The Enterprise is the only ship that is still sailing. You'll also learn of the Nepto Shrine, the building on the cape. An old man here will be able to tell you more about it.
The map says the chest in the hidden passage at the entry level has Soft, but it's really 300 Gil.
The door to the north here has an all-in-one magic shop (Red Mage), item shop (guy to the right) and inn (woman in the center).
Go up the stairs and go left, then enter the south wall to find a hidden passage. The stairs at the other side lead to the old man you were told about. He tells you that the Nepto Shrine is where the dragon Nepto used to sleep, but the earthquake has driven Nepto mad. You can heal with the waters to the right.
To the right of the second floor stairs is a hidden passage. Go right after entering to find the true path to the chests that contain Fire2, Bolt2 and Ice2.
On the second floor, you'll find out that if you go past the cape, Nepto will attack. Another guy says that if you get rid of Nepto, you can have the Enterprise. From there, you can head north up the stairs and get back to the overworld. Do not get in the ship to travel the waters. You won't be able to get far, as you'll soon meet Nepto, who will tear your party to ribbons.
Instead, walk north and west to enter the Nepto Shrine.
You'll want to be Mini the entire time you're here. Press A at the statue and you'll enter through the hole in the right eye.
The Liliputs and Puti can easily be defeated with Level 1 spell charges. The Putis can cast some nasty spells, so take them out as soon as possible. BloodWorms will need Level 2 charges to bring down more efficiently.
At the end of the hallway, the left hall will lead to the Carapace Helm and Armor, while the right will lead to a Serpent Sword and the boss.
You'll face the Big Rat, and it won't give its gem to anyone. Hit it with Level 2 spells, and you should be able to finish it off quickly. You'll be able to obtain the Nepto's Eye when you're done. Go back to the entrance and plug the hole where the eye should be with Nepto's Eye. Nepto will thank you for returning the gem and returning his mind back to him. He rewards you with the Water Fang, which smashes obstacles in your path with the power of Water.
You'll then find out the Water has lost its Light, and the earthquake that caused the Light to be sealed underground may be the work of an external force. Looks like we have another Crystal to find...