After falling through a hole in a cave behind Ur, Luneth learns from an ominous crystal that he is to seek out three other Warriors of the Light in order to restore balance to the world. When he returns to his home, he learns from Elder Topapa that he was brought to Ur by a man whose clothes were covered in ashes and burns, later revealed to be Cid Haze.
Luneth, along with his loyal friend Arc, travels to the neighboring mining town of Kazus. They are horrified to find that the resident of Kazus have been turned into ghosts by an entity named Djinn, who was released from his bonds by the previous earthquake. After meeting with Cid, they go his airship in the desert, which Refia is stealing in order to travel to King Sasune's castle in order to retrieve his mythril ring to rid the townspeople of their curse.
Upon arriving at Castle Sasune, Luneth meets Ingus, a loyal knight that was fortunate enough to be away from the castle when Djinn's curse hit. After an audience with King Sasune, the party travels to another Cave where Princess Sara is tracking down Djinn in order to vanquish him and dispel the curse on her kingdom. The party then confronts Djinn, and, with Sara's help, destroys him for good. But after Djinn dissapates, Luneth, Arc, Refia, and Ingus are teleported to the Wind Cave with the crystal, revealed to be the Crystal of Wind, unlocking the first set of jobs. Ingus then returns to his castle to tell his king of his quest, and apologizes to Sara, his dear friend. King Sasune gives them their foldable canoe, which they use to retrieve the airship from the cave's entrance.
The party then takes the airship back to Cid in Kazus, when Refia is soon whisked away by Takka back to the forges. Cid then joins the party to destroy the boulder that fell and blocked the passage to the southern continent and return to his wife in Canaan. Takka then makes a mythril ram for the airship, where Refia is once again hiding in. The ram destroys both the boulder and the airship. The party then realizes that they are all orphans, each chosen to be a Warrior of the Light.
In Canaan, after healing his ailing wife, Cid tells the party to seek out King Argus if they want a second airship, as he only built the hull. Refia learns of a poor girl named Salina, who wishes to see her boyfriend, Desch again. After speaking with several villagers the party learns that Desch went to Dragon's Peak. Luneth suggests that they follow him to bring him back to Selina.
After being capture by the dragon, the party meets Desch, a young man who has lost his memory. The party flees from the dragon with him, and he is scolded by Refia, who demands to know why he left Salina. Desch give the spell Mini to the Warriors, and joins them as a guest.
In the village of Tozus, the gnome doctor gives the party access to the path to the den of the Vikings. The party sets out with the vikings last ship, the Enterprise, in order to slay the Nepto dragon the plagues the seas. Instead they go to the temple dedicate to the sea god Nepto, where they find a statue dedicated to the god missing one of its ruby eyes. After traveling down a tunnel in the statues mouth and retrieving the missing eye, the party learns that the eye houses the god's soul, and the only thing that allows her to control her physical form that plagues the Vikings. She gives them the Fang of Water, and returns to her eternal slumber. As a show of gratitude, the Vikings give the party the Enterprise, and their journey continues.
Using the Enterprise, the party takes Desch to Gulgan's Gulch to speak to the blind oracles. Desch is told to go to the Tower of Owen in order to retrieve his lost memories. (The player can also go to the Village of the Ancients for more information on the continent, take Desch back to Canaan to see Selina, and go to the village of Tokkal to discover more). During the climb up the Tower of Owen, Desch reveals that he is actually an Ancient charged with guarding the tower. After facing Medusa at the top, Desch leaps into the tower's flames in order to keep the continent from crashing into the planet underneath. His final words to the party are "Seek the Crystal of Fire on the island of the Dwarves!". The maelstrom blocking the party from the outer edges of the continent disappears, and the party goes to the outer edges. A question rises to the player: Who is Xande?
On the Island of the Dwarves, the Warriors learn that the rouge dwarf Gutsco has stolen one of the Horns of Ice, and has fled into an underground lake. After defeating the rouge, the party resurfaces, where the same dwarf steals the second horn. The party follows him to the Fire Cave and defeat him again. The Crystal of Fire then gives them its powers, unlocking the second set of jobs. The Horns of Ice are returned to their altar, overjoying the dwarves. A resident of the recently plundered town of Tokkal stumbles in, begging the Warriors for their help in saving the town.
In Tokkal, the entire party it incapacitated by Hien's men, and taken to the fortress inside the Elder Tree of the Living Woods. After defeating Hien and return the Elder Tree to its rightful place, King Argus gives the party the piece of an airship Cid needs. Everyone returns to Canaan.
Cid tells everyone of their true origins: They are all residents of the Continent below their current home. Cid tells him that on an airship trip while they were children, a darkness engulfed the ship that caused it to crash and catch on fire. Cid, Refia, Luneth, Arc, and Ingus were the only survivors. Cid turns the Enterprise into a ship/airship. The party decides to return to their home to discover where they came from.
When the party uses the Enterprise to go to the edge of the continent, they are engulfed in a darkness. Upon locating a beached ship, they meet Aria, a priestess of the Water Temple. After giving her an Elixir she reveals that time has frozen for the entire continent, but if they restore power to the Crystal of Water, time will return to normal. Aria then joins the party as a guest. After the Warriors of the Light trek through the Cave of the Tides to reach the crystal, Aria stands before it and begins to pray, restoring its power. Suddenly, the Kraken strikes. In an attempt to save Luneth, Aria blocks the Kraken's attack and gives the party time to defeat him. Sadly, Aria dies of her wounds.
The Warriors awoke to a woman saying "Seek Doga on the Dalg Continent". They found that the Enterprise was locked up by Goldor had locked the Enterprise under a gold chain so the Warriors, whom he believes are the Warriors of the Darkness, cannot steal his Earth Crystal. Upon defeating Goldor, he breaks the Crystal, saying if he can't have it, no one can! The party grabs the key and unlocks their ship.
...to be continued