The story takes place in your typical Medieval European Fantasy worldnote except that this one is sustained by four elemental crystals. When the wind begins to slow downnote , the King of the Land of Tycoon, who is in charge of protecting the Wind Crystal, decides to go check out the Wind Crystals Shrine, despite his daughters (Princess Lenna) protests. When the wind stops completely, she sets out on her own to find him, only to be knocked out by a large meteor that just happened to crash nearby.
She is found and revived by a wanderer named Bartznote ; they also find an old man, also knocked out by the impact, who suffers from amnesia as a result; he only remembers that his name is Galuf. The three of them set out for the Wind Shrine, but are captured by pirates. However, the Pirates captain, Faris, notices that Lenna is wearing the same pendant as he is, and suddenly decides to join them in their mission instead. note
When they reach the Wind Shrine, they find the crystal shattered, and a ghostly vision of the King urges them to save the other ones before the world dies. The spirits of ancient heroes inside the crystals shards grant them their powers so they can accomplish this mission.
After many tribulations (during which they discover that Faris is actually a woman) the group reaches Walse, the Kingdom that holds the Water Crystal. There they find out that what is weakening the crystals are machines designed to extract more power from them. Also, a normally-harmless creature attacks the crystals tower. The heroes are unable to prevent its destruction, though they do gain more crystal shards.
On Karnak, the Kingdom of the Fire Crystal, the group meets Cid, the inventor of the machines that are damaging the crystals. He only wanted to do good and is very contrite about the results. But before they can save the crystal they are interrupted by the very queen of the land who (later) explains that she had been possessed by an evil being that seeks to free itself from a prison maintained by the crystals.
Only the Earth Crystal remains by now, but no one knows where that one is located. Cid (and his grandson, Mid) help by creating vehicles for the heroes, as well as discovering that the last crystal is hidden in a desert ghost town. There the group finds King Tycoon, but hes under the evil spirits control and attacks them. They are saved however by the arrival of a girl named Krile who turns out to be Galufs granddaughter; finally regaining his full memories, Galuf reveals that he is from another planet (the meteors are actually disguised spaceships) and that he and three other warriors came here decades ago to capture and seal the evil sorcerer Exdeath with the crystals.
The last crystal shatters and Exdeath is released. King Tycoon dies saving the others. Exdeath returns to his original world. Galuf and Krile return to fight him there; the other heroes soon decide to follow and aid them, using resources from the other three meteors that landed (their pilots were all killed.)
On Galufs worldnote the three heroes are captured by Exdeaths forces (including the Ineffectual Sympathetic Villain Gilgamesh) and Galuf has to rescue them. Eventually they learn Exdeaths origin: its actually a tree that came to (evil) life after the forest it was part of was used to seal evil spirits. What it is after is the ultimate power, a force known as the Void. Its sealed between Bartzs and Galufs worlds- which are actually the same planet, split in two in order to seal the Void in between them. By destroying the crystals on both worlds, Exdeath can get access to it.
The heroes not only fail to save this worlds crystals too, but Galuf dies saving the others. Krile takes his place in the team, inheriting his powers. In fact all of the surviving, original Dawn Warriors die in the process of fighting Exdeath (Bartzs father turns out to have been one of them). With the Four Dawn Warriors gone, the party travels to Exdeath's castle and take him on. After a grueling battle, they successfully destroy him, but he uses his magic to shatter the final crystal. With the crystals shattered and Exdeath gone, the two worlds merge into one and the day appears to be saved.
Awakening near Tycoon Castle, the party are found by the castle's occupants, who throw a party for the return of Princess Sarisa. Bartz goes a little bit gaga over her, but ultimately leaves with Krile, both feeling out of place in the royal party. After a short journey, in which Krile notes she has a splinter, the party are trapped in a pit caused by the unstable land that the merging worlds is creating.
Bartz and Krile are rescued by Faris, who has gotten rather tired of being a princess, and they set off for the Ancient Library, hoping to find a way to defeat Exdeath. Ghido is as condescending to Bartz as ever, but they come to the conclusion that the only way to stop Exdeath once and for all is with the help of the Twelve Legendary Weapons.note These weapons are sealed away in the Sealed Castle, and require the four seals hidden around the merged world to release.
But Exdeath returns, having hidden out as the splinter in Krile's hand, and attempts to take out Ghido. Ghido, however, fights him to a total standstill and forces Exdeath to leave, but not before Exdeath reveals he has gained power over the Void, and he demonstrates this new power by opening Void portals in several locations around the map, including over Tycoon, with Lenna still inside. Now enraged, Faris and the party head off to find the seals.
The first one is in the Great Pyramid of Moore, and the trio have little trouble retrieving it. On their way out, they discover that Hiryu rescued Lenna from the Void portal at Tycoon, but that Lenna hs been possessed by Melusine. The trio are able to banish Melusine, and the trio becomes the New Four Dawn Warriors once again. The party continue to locate seals and unseal the Twelve Legendary Weapons, but Exdeath strikes again, opening more Void Portals, including over Bartz's home town of Lix. Now with everyone having personal stake in the battle, the preparations are redoubled. The party retrieves Syldra and Phoenix as summons, unlock the Flare and Holy magicks, and strengthen themselves to be ready for the battle.
Once ready, the New Dawn Warriors enter the Tycoon portal to try to stop Exdeath. Exdeath throws every monster of the Void that he can at the party, but the party are too strong and make their way through the various consumed locations, eventually coming across Gilgamesh in the Void. Gilgamesh had been stuck there since Exdeath banished him way back on the second world, and now he just wants out. Bartz and the party point him the right way, and he leaves, thankful for the aid. However, the party soon find themselves outmatched by the monster Necrophobe, and Gilgamesh returns to save them, sacrificing himself to destroy Necrophobenote .
Finally, the party confront Exdeath, who pens several more portals on the world, consuming more of it, and demoralizing the party. But the original Four Dawn Warriors and the King of Tycoon show up to embolden them once again, and they enter a battle with Exdeath, who is using the full power of the Void. But the party is just too strong, and the Void takes possession of Exdeath itself, creating Neo-Exdeath, who wants nothing more than to destroy everything and return it all to the Void. After a mighty struggle, the party destroy him once and for all, but all is lost and has been consumed.
In the darkness of the void, however, the four spirits of the Crystals are able to reform, once again protecting the world, eliminating the Void's influence, and saving everyone, but any party members lost in the battle are gone for good.
A year later, Krile (or Bartz, then Faris, then Lenna in that order, if all previous writers have fallen) is writing to Mid, talking about how the world has changed. If they survived, Lenna is back in Tycoon, Faris cast aside the life of royalty and still lives as a pirate, and Bartz has been wandering. Krile ends up at the Guardian tree on the anniversary of Galuf's death, sad and alone. Any fallen party members are revived, any others join her so that she isn't alone, and they all vow to continue protecting the Crystals.
Note: the Game Boy Advance version of the game has an extra dungeon with a special Boss, Enuo, the first being to try to harness the power of the Void (and thus indirectly responsible for all that happened in the game) but this is only available after the game ends (and is only an optional Side Quest) so it may not count as part of the story.