The game begins with four orphans who decide to explore a cavern opened up by an earthquake. They are set upon by monsters. When they arrive at the end of the cave, they discover a crystal. The orphans are then attacked by a giant turtle, but manage to defeat it, receiving the light of the Wind Crystal and getting the first jobs.
Returning to their home town, they meet their adoptive father Topapa. He tells them that he believes that they are the four Warriors Of Light, and that they must find the other crystals. Unfortunately, they are blocked off from the outside world by a large rock. It could be broken by an airship crashing into it, but the person who could fit a metal bow onto it has been turned into a ghost along with everyone else in Kazus and Sasune. The one who did this was a monster called Jinn, and according to the King of Sasune, the Princess Sara has gone to seal him. A ghost named Cid gives them his airship, hidden in the desert west of Kazus, in order to reach the cave.
Inside the cave, the party allies with Princess Sara. The orphans defeat Jinn, and Sara seals him, tossing him into sacred water at Sasune to turn everyone back into people. Back in Kazus, the metal bow is fit onto the airship, and Cid and the orphans fly it straight into the rock, destroying the rock, but taking the airship with it. The party take Cid to Canaan and cure his sick wife Granny. Atop a mountain to the east, they meet an amnesiac known as Desch and a dragon known as Bahamut.
The party jumps down the mountain, and turn themselves into midgets to get through the Hidden Road in the midget town of Tozas. They arrive at the Viking Base, where the Vikings agree to give them a ship if they can calm the wrath of Nepto, the sea monster. The party become midgets again and enter the statue of Nepto, finding the Crystal Eye that fell down. The party restore it to the statue and Nepto is calm again.
In the ruined town of Tokkle, the party meets the Gulgans, blind sages who can see into the future. They tell the orphans that Desch's destiny lies in the Tower of Owen to the east. At the top of the tower, Desch remembers that he is the Guardian of the tower and sacrifices himself to keep the Floating Continent in the sky. The whirlpool stopping the party from proceeding is stopped.
The party sails to the Dwarf Cave, there they discover that the dwarves' sacred relics, the two horns, have been stolen by a man named Guzco. They regain the horns from Guzco, who hides in their shadows and steals the horns again. The orphans follow him to the Cave of Fire, and defeat him when he transforms into Salamander. They receive new jobs from the Fire Crystal, and the Dwarves tell them that they must defeat Hyne in order to save Tokkle.
Back in Tokkle, the party are imprisoned by Hyne's soldiers and taken to his castle. They manage to break out of prison and kill Hyne. Castle Hyne returns to the forest it originally was, and go and get the Time Gear that can change their ship into an airship. They use it to fly to a Shipwreck, where they meet Elia Bennett, the Maiden Of Water. She lowers the water level in the Cave of Water, but is shot by a deadly arrow fired by Kraken. The heroes defeat him to avenge her, and receive jobs from the Water Crystal. The world is flooded and the airship reverts to a ship.
However, while they were doing that, a person named Goldor has chained up their ship. In order to reach him, they need to get the Floating Shoes. In the sewer, they save Four Old Men who are pretending to be the Light Warriors, and get the shoes from an old woman called Delila. They cross a swamp to Goldor's Mansion, and defeat him. He shatters the Earth Crystal, which turns out to be a fake. They destroy the chain on their ship by touching an enchanted key he left behind.
Using the airship again, they fly near the nation of Salonia, where their airship is shot down and they land in the middle of a civil war. In a pub, they meet a young boy named Allus, who is the Prince. However, some thugs who don't believe him are bullying him, and have a bar brawl with the party (in the form of a normal battle). Allus joins the party, and the group sneak into the castle. But while they sleep, King Gorn comes in and tries to stab his son. Allus frees Gorn from being mind controlled by his advisor Gigames. Gigames reveals himself as the monster Garuda, and is defeated, but manages to kill Gorn. Allus says goodbye to his father, and becomes King.
The party gets the Nautilus, and flies to the house of wizard Dorga. He reveals that the true villain is Zande, who studied with Dorga and a woman named Unne under the archmage Noah. Dorga was given Noah's power, Unne got control over the dreamworld, and Zande received mortality. Zande suffered from a fear of dying, and decided to destroy the crystals to return light and darkness to the Void, where he would be safe from death. In order to stop Zande, the party will need to enter the Slyx Tower.
Dorga sends the party to find Noah's Lute so that they can awaken Unne and get the airship of Invincible. When they get into the Temple Of Time and get the Lute, they search for and awaken Unne. She leads them to the Invincible, which they use to enter the Cave Of Darkness. They take the Earth Fang, and use the four fangs they have collected throughout their journey to destroy statues blocking a path. At the end of the path, they find Dorga and Unne. They are forced to defeat Dorga and Unne to get keys to enter the Sylx Tower and the Forbidden Land Eureka.
In Eureka, the party discovers two more jobs (presumably from broken-off crystal shards), Ninja and Sage, along with five ultimate weapons. The party reaches the top of the Sylx Tower and are paralyzed by a curse. Dorga's ghost brings Cid, Desch, Sara, Allus and one of the Four Old Men (seems Elia's ghost wasn't on hand) to break the curse. The party defeats Zande and are subsequently attacked by a monster named the Cloud Of Darkness.
The orphans cross over into the Dark World, freeing the previous warriors (the Warriors Of Darkness) and the Dark Crystals. Finally the Dark Warriors overwhelm Cloud of Darkness, allowing the heroes to take her down. The party use their airship to take the Old Man, Allus, Desch and Cid back home, but Sara decides to go back with them. The party are reunited with their family and friends back in Ur.