An earthquake opens up a previously hidden cavern in Altar Cave near the village of Ur on the Floating Continent. Four young orphans explore the new cave, fighting a monster which turns out to be a test of strength from the dying Wind Crystal. Dubbing them the Warriors of Light, the crystal grants them the last of its power and instructs them to restore balance to the world. The Warriors set out to explore the Floating Continent, which has seen increased attacks from monsters. On their journey they aid the princess Sara in pacifying a rogue djinn, find Desch during a quest to destroy a tower threatening the region, and gain access to the airship Invincible from Cid. The Warriors also receive power from the Fire Crystal, which is under attack from servants of the mage Xande.
After gaining the Invincible, they go beyond the Floating Continent for the first time in their lives, finding the surface world almost entirely flooded. On the surface, they complete further trials, receive the blessing of the Water Crystal, and help Alus reclaim his kingdom from his possessed father. The warriors then meet with Doga and Unei, who reveal Xande resents the gift of mortality their master gave and attacked the Crystals to halt time's flow, an attack which caused the Wind Crystal to raise the Floating Continent to safety. Gaining the final blessing from the Earth Crystal, and taking keys from Xande's most powerful servants, the Warriors and their allies break into his stronghold the Crystal Tower.
The Warriors of Light defeat Xande, but are too late to stop the imbalance he started, which summons the Cloud of Darkness who absorbs Xande and states its intent to return existence to the void. The Cloud of Darkness kills the Warriors, but Doga and Unei sacrifice themselves to revive them, allowing the Warriors to enter the world of darkness where the Dark Crystals reside and ally with the original Warriors of Darkness. The Warriors of Darkness sacrifice themselves to weaken the Cloud of Darkness, allowing the Warriors of Light to defeat and drive it back. The Crystals are revived and the world's balance restored, and the Warriors and their allies return to their old lives.
