Storyline
On a Floating Continent above the old world, an advanced civilization wanted to control the power of the four crystals of light. They did not realize that they could not hope to control the power of them. This disrupted the balance of light and dark, so four warriors were granted the power of the dark to return everything to equilibrium. The Dark Warriors succeeded in their quest and restored harmony to the world, but they were too late to save the civilization that had tried to harness the power of the crystals. All that was left was ruins, though their floating continent remained. On that very continent, the circle of Gulgans, a race of blind soothsayers and fortune-tellers, predicted that eventually things would come full circle. Just as the power of light can be abused, so too can the power of darkness. And when that occurred, the crystals of the light would call forth their own champions to restore balance to the world.
One day, Luneth falls down a tunnel and discovers the Crystal of Wind. After receiving his task, he goes to find his friend Arc, and together they journey to Kazus, the village cursed by the Djinn. They seek out Refia, and all three journey to Castle Sasune to see the King and retrieve the Mythril Ring. They are granted access by the royal guard Ingus, who becomes their fourth companion.
The four journey back to Kazus and enter the Sealed Cave. There they find Princess Sara, who has the Ring and they are able to defeat the Djinn. She returns to the castle while they are transported to the Altar Cave, where the Wind Crystal bestows upon them its light and several Jobs, and officially makes them the Warriors of Light. They are instructed to restore the other crystals and bring equilibrium back to the world.
Back at Castle Sasune, Princess Sara uses the Mythril Ring to break the curse and free the people. The warriors then go and find Cid in Kazus. He uses his airship to aid them in destroying the boulder in their path. Unfortunately, it destroys the airship, rendering the party land bound until they can find a ship.
They then journey to the town of Canaan and meet Cid's wife and a strange girl named Salina. She mourns the disappearance of her love, Desch. The four then journey to Dragon's Peak where he was last seen. After scaling the peak, they encounter and are kidnapped by Bahamut, who drops them off at its nest. There they encounter the mysterious Desch. They learn that he has lost his memory, and so he decides to join them.
The group heads for Tozus next, the village of the gnomes, to reach the Vikings Cove, where they may acquire a ship. However, they find the Vikings in an uproar as their feared water deity, the Nepto Dragon, has become wild and angry. The Viking Chief requests the warrior's aid. They journey to the Nepto Temple, and they find that an idol of the Nepto Dragon is missing an eye jewel. They eventually find the missing eye and take the eye to return the eye to the socket it was stolen from, and appease the angry Nepto Dragon. In gratitude, the Vikings bestow upon the party the Enterprise.
Sailing upon the Enterprise, the heroes then explore the continent. They travel to the Village of the Ancients, and learn that the continent they are on is actually floating above the old world. They eventually find the Tower of Owen and begin to explore it. When they reach the main room, they find Medusa waiting for them. After defeating her, Desch's memory comes back. He recalls that he is one of the ancients who was the Guardian of the Tower tells the warriors that the tower is the force keeping the floating continent up. As it threatens to fall, Desch leaps into the central furnace to stop it from falling.
They head for Dwarven Hollows, in search of the Fire Crystal. The dwarves are preoccupied because one of their precious ice horns was stolen by Gutsco the Rogue. They follow him and after "defeating" him, they make their way back up to Dwarven Hallows, followed by a mysterious shadow. When they reach the main altar, Gutsco reveals himself and grabs both horns. The four pursue him again, this time into the Molten Cave. Gutsco leads them straight to the Crystal of Fire, whose power he absorbs. He turns into a dragon and the battle ensues. After defeating Gutsco a second time, they receive the Light of the Fire Crystal and several additional jobs, and return the Horns of Ice.
The Warriors of Light sail then to Tokkul. There they learn that the evil Hein, adviser to King Argus, has captured the King, enslaved the people, and uprooted the Elder Tree from the Living Woods. They are attacked and kidnapped by Hein's men, and taken to Castle Hein, which is actually the floating Elder Tree.
The Warriors of Light restore the Elder Tree and King Argus thanks them for their deeds. They receive the Wheel of Time take it back to Cid, who transforms the Enterprise into an airship. He also tells them the four of them are not from the floating continent but are instead from the world below. The four travel back to the world below. They then meet Aria, one of the last remaining Priestesses of Water, who recognizes them as the Warriors of Light. She asks if the world is no longer frozen and hearing that it is not restored, journeys with the warriors to the Temple of Water and recovers the shard of the Water Crystal. Using the shard, she opens the way to the Cave of Tides. She instructs the warriors to return the light to the crystal. As they approach, Aria suddenly pushes Luneth out of the way of a blast of magic. She falls, and Kraken reveals himself. The four battle him, and once he falls, light is restored to the Crystal and the World is returned to normal, as Aria slowly dies.
In the new world, the four awaken in the Town of Amur. They find their ship tied with a chain, and so journey to Goldor's Mansion to retrieve the key and the Fourth Crystal. Goldor shatters the crystal, but drops the key. They return to Amur and free the Enterprise.
They fly around, visiting several towns, but are shot down over the Megalopolis of Saronia. They find the kingdom in uproar. They find the King's son, Prince Alus in South west Saronia, who has been banished from the castle by his own father. Arc convinces the rest to aid him. The king kills himself and is immediately free from the spell placed upon him by Garuda. They fight and kill Garuda, and Prince Alus becomes the new king.
Shortly afterward, scholars inform the party that the airship Nautilus has been unearthed. Using it, they go meet Doga at his Mansion. He leads them to Unei, the guardian of the dream realm. She happily joins the party and together, they go to the Ancient Ruins and manage to take control of a large airship called the Invincible and she leaves the party. When the party travels to the Cave of Shadows, they find the Fang of Earth, and they head back to Doga's Manor to visit Doga and Unei. Upon entering Doga's manor, they are teleported to a cave where Doga and Unei are waiting. There, they tell the Warriors of Light to defeat them in battle. Reluctantly, they do as they are told and are explained why they were needed to be killed. As it turns out, their souls were needed to power the keys needed to open the forbidden land of Eureka and Crystal Tower.
Before entering the Crystal Tower, they go through the Maze of the Ancients, which is where the final crystal was held. After receiving said crystal, the warriors travel through the Crystal Tower and attempt to cross over to the Dark World. Before crossing, they find themselves under the curse of the Five Wyrms, which holds the party locked in place. Doga remedies this by finding five past allies of the warriors to break the curse. The five allies are Princess Sara, Cid, Desch - who did not die upon hurling himself into the tower, King Alus, and one of the four old men from Amur. After interrupting the curse, the allies wishing the Light Warriors the best of luck, and the heroes reach the portal to the World of Darkness.
In front of the black vortex, the warriors confront Xande and defeat him. After he dies, they face the Cloud of Darkness, who was manipulating Xande without his knowledge to reduce the world to nothingness. They fail to defeat their enemy and are killed by her particle beam in the process. Fortunately, with the light of the five allies that had helped them before, they are revived and continue into the World of Darkness. Within, they defeat four malevolent beings, who were guarding dark counterparts of the crystals. These crystals reveal the four Warriors of the Dark, who stopped the Light from engulfing their world many years ago.
When they all face the Cloud of Darkness again, the four Warriors of the Dark sacrifice themselves so that the Warriors of Light are able to defeat their adversary. With one last battle, the Cloud of Darkness is defeated and the heroes and their allies all return to their homes. The old man returns to Amur, Alus returns to his kingdom, and Cid and Desch return home to their lovers. Sara on the other hand, does not want to leave Ingus, and stays with him a while longer. Each of the heroes end up going their own ways, with Ingus and Sara returning to Castle Sasune, Refia taking up blacksmithing again in Kazus, and Luneth and Arc returning to Ur. This conflicts slightly with the Famicom version, in which all of the main characters returned to Ur together.