Atop Mt. Hobbs the group rescues the monk Yang Fang Leiden from the attacks of a pack of monsters.
Yang, native from Fabul, decides to join them and warns his king of Baron’s incoming attack. While Cecil and Edward, together with the other monks, defend the castle and the Crystal of Air, Rydia and Rosa are told not to get involved in the forthcoming battle.
Unfortunately the fight doesn’t end in favour of Cecil. In the Crystal Room Kain, for an unknown reason, turns against Cecil and attacks him. When the duel is won by Kain, he takes the Crystal leaving Cecil behind. At the same time both Edward and Yang are defeated by a man called Golbez, who also takes Rosa as hostage.
With both the Crystals and Rosa in Kain’s hands, Cecil decides to follow him. Given that Baron’s navy is far weaker that its air force, Cecil suggests to reach Baron by sea and then sneak into the town. Rydia heals the party and they prepare to leave.
The king of Fabul donates a ship to the group so that they can continue their quest for the crystals (and Rosa). Shortly after their departure, the ship is caught in a huge whirlwind that appeared right beneath it. Leviathan, also known as the Lord of All Waters, attacks the vessel and makes it move to and fro. Since the ship is rocking a lot on water, Rydia falls overboard. Yang tries to rescue her before it’s too late but he ends up falling overboard as well.
Leviathan’s attack scatters the group and for a while it is unknown what has happened to Edward, Yang and Rydia. When Cecil finally regains consciousness, he finds himself on the shore near Mysidia. There he is told by the Elder that to defeat Golbez he has to hand over his dark sword. As a consequence he heads to Mount Ordeals in order to become a Paladin; accompanied by two mages, Palom and Poron, Cecil successfully completes his challenge. On Mount Ordeals he also reunites with Tellah, who joins the party. After attaining his Paladin status, Cecil returns to Baron using an hidden passage called The Devil’s Road.
In the meanwhile Yang wakes up on a shore near Baron and, due to an amnesia caused by Leviathan’s attack, he enlist as officer in the local army…unaware he is on the enemy’s side. After a short fight against Cecil, Yang eventually snaps back to reality and informs the party on Rydia’s fate, telling them he wasn’t able to grab her after she fell.
With one Crystal left to find, Kain proposes to Golbez to have Cecil retrieve it in exchange for Rosa. Cecil accepts Kain’s conditions and together with Tellah, Yang, and Cid he begins to search for the Crystal of Earth. While they keep a look out for the Crystal, they arrive in Troia where they meet Edward, who recovered there. Like Yang, Edward is unaware of Rydia’s whereabouts and haven’t seen her since Leviathan’s attack. Since Yang last saw Rydia being swallowed, the group draws the only possible solution: that she was killed by Leviathan.