With the Crystal Rod in hand, it's time to head to the Mysidian Tower. It can be found on an island to the North of Mysidia that almost makes a circle, with an opening along the south. You'll have to hop on your ship and head over to it. But as you approach the opening, a whirlpool will suddenly appear, and suck your ship to the bottom of the ocean. (If you are concerned with keeping any of Leila's equipment, remove it before you approach the island.) When you awaken, you will discover that Leila's missing. You are now in the bowels of an aquatic beast known as the Leviathan.
The Leviathan
You begin in the intestinal track of this large beast. From your starting point, you must walk along a linear path until you find a way to get higher up into the creature. Along the way, portions of the floor will be lined with digestive fluids. These fluids are acidic and do slight damage to the members of your party as you walk through them. You are forced to walk through them, so minimize your route to avoid taking more damage than necessary. All the while, you will be attacked by the creatures who make the beast their home. Along the way, you will find two chests, the first containing the Twist Headband, and the second has a Power Vest. Be sure to equip these power items on whoever they benefit most.
When you reach the next level, you may be surprised to find other people about. One of the first you will encounter is an armored warrior. He will ask who you are, at which time you may ask him about anything. If you happen to ask him about Dragoons, he will confess that he is one. But when you tell him the news about Dragoons and Wyverns, he won't believe you. Present the Crystal Rod to him, and he will understand that you were after the Ultima Tome as well. He proposes that you might be able to defeat the large monster guarding the exit if you team up. At that time, he will join you. His name is Ricard, and he specializes in spears.
After that, explore the rest of the area. All the other people present will explain that you're in the Leviathan's stomach, and there are apparently several Crystal Rods, as the Leviathan eats anyone who has one and tries to enter the tower. There is a chest near the top which contains a Power Armlet, another defensive item which also increases your attack power. Make your way to the upper left corner where you'll find a passage to another level.
You are closer to the Leviathan's mouth. As a result, on this next level you'll find differently colored, but no less dangerous saliva. Walk through it carefully. There are two chests on this level, one on the top which contains the Gaia Blade, and one on the bottom which has a Diamond Shield, but leads to a forced fight with some Red Souls. Be sure to equip the Gaia Blade for anyone who is strong with swords. Then head left and approach the monster at the mouth of the Leviathan. Heal anyone if necessary, and then speak to the monster.
The monster is a Roundworm and it's blocking access to a boat which you can use to escape. Naturally, you must defeat the Roundworm to proceed. No special strategy is required, the Roundworm is simply very strong defensively and offensively. You'll need really powerful attacks to do damage, and his bite will do quite a bit of damage to you. Most of your party should be well trained and strong enough to withstand it, but Ricard may still be fairly under powered for this fight, and can die with one hit, so be sure to have a member who can cast Life handy, or some Phoenix Downs just in case. Blink and Protect will help as well.
The Tower of Mysidia
Once the Roundworm is defeated, you can freely sail in and out of the inlet. Park your boat in front of the tower, (save your game,) and approach. When you do, the Crystal Rod will remove the barrier surrounding the tower, and allow you to enter. If you do not have a large supply of healing items, you may wish to consider heading back to Mysidia or Altair to stock up; the tower has many floors and is quite long.
On top of the tower there is a golden crystal containing the Ultima spell, but also four grey (silver?) crystals that maximize one attribute each.