The Great Forest of Moore was a place to where all evil souls were banished, trapped forever under the seal of the Sage Tree. The souls trapped in the forest eventually fused with each other, giving birth to a large tree. This tree acquired self-consciousness, and started calling itself Exdeath. Exdeath left the forest and plotted the downfall of mankind, to create a world of evil. For this end, Exdeath sought to control the power of the Void, which had been sealed in the Interdimensional Rift years before. The only way to do this was to destroy the crystals that supported the seal, so he went to the second world to destroy the crystals there. However, Exdeath was faced with the four Warriors of Dawn, which had been chosen to protect the crystals. They defeated him, but were forced to seal Exdeath in that world, using the power of the four crystals from that world. The years passed, and the humans started to abuse the powers of the crystals. This not only weakened their power, but also the seal over Exdeath. Being able to project his consciouness, Exdeath started manipulating people, so the crystals would shatter and the seal over him would be released. Knowing this would happen, Galuf, one of the Warriors of Dawn, traveled to the second world into a meteor to prevent Exdeath from breaking the seal. However, he lost his memory when the meteor felt. He is found by Bartz and Lenna, who all go after the wind crystal, later joined by Faris, who uses her ship to travel everyone to the wind shrine. However, they arrive too late, as the crystal had already shattered. They then decide to protect the remaining crystals, being chosen by them as the new Warriors of Dawn. Their efforts are futile, however, as all crystals shatter and Exdeath breaks free. Exdeath resumes his plan, going back to the first world. Galuf, who had already recovered his memory, goes after him. Bartz, Lenna and Faris manage to travel to the first world to go after Exdeath.
As they arrive, they are captured by Exdeath's minions. Exdeath leaves his right-hand Gilgamesh keeping an eye over them, as he starts the activation of a force field over his castle. Galuf sneaks into the castle and fights Gilgamesh, who flees. They run away from the castle, and are confronted by Gilgamesh again at the Great Bridge, but he once again flees. Just the, Exdeath finishes the activation of the field, which sends them all flying to the northern continent. They are later rescued by Krile, Galuf's granddaughter, who tells them that the sage Ghido was calling for them. They arrive at Ghido's island, but Exdeath floods the island to stop them. They eventually learn that Zeza, one of the original Warriors of Dawn, took a fleet to shut down the force field on Exdeath's castle. Zeza takes them by submarine to an underwater cave behind the castle, which connected with one of the towers that powered the field. They climb the tower and destroy the antenna after Zeza shuts it down, but the generator room starts self destructing, killing Zeza in the process.
Using Zeza's submarine, they go after Ghido, who tells them that Exdeath is after something in the Great Forest of Moore. The four go to the forest, only to see it being burnt to ashes. They find the Sage Tree in the remains of the forest, and without knowing they break the seal on the four crystals of that world. Exdeath then enter the tree and claims the crystals for himself, using their power to trap the heroes. Krile also arrives and knocks Exdeath, but he just traps her as well. Furious, Galuf uses all of his strength to break free, shattering one of the crystals and knocking Exdeath. Exdeath fights back, but even using all of his strength he is unable to hurt Galuf, who ends defeating him. Over exausted, Galuf uses his last strength to free the others, but ends dying in the process. Exdeath retrieves the crystals and flees to his castle, so Bartz and the others go after him. Once in the castle, they are confronted by Gilgamesh again, who just can't seem to defeat them. Infuriated with his incompetence, Exdeath banishes Gilgamesh to the Interdimensional Rift. Bartz finally faces Exdeath, but as he defeats Exdeath, all remaining crystals shatter, causing the two worlds to become one again.
Bartz, Faris and Krile eventually find Ghido again, who tells them that now that the world has become one again, the portal to the Interdimensional Rift will open, allowing the Void to escape. Exdeath, who was disguised as a splinter, shows himself and thanks Ghido for the useful information, since this was his objective all along. With the two worlds united again, he would be able to take control over the Void. Just to show them the power of the Void, he opens the portal to the rift over the Tycoon Castle, where Lenna was. Ghido fights him, but Exdeath sends them away. Ghido then instructs them to look for the twelve ancient weapons that had been used to defeat the evil wizard Enuo, who created the Void. Inside the rift, Exdeath makes a deal with all the monsters there, who become his minions.
When Bartz, Faris and Krile comes to the Sage Tree, Exdeath attacks them, this time sending Lenna, who was possessed by a monster from the Rift. Lenna's dragon rescue her by taking the demon out of her body, so Bartz and the others defeat it. As they leave the place, Exdeath starts spreading the Void everywhere, destroying various town, which makes Bartz become furious. They manage to collect all the legendary weapons, then enter the Interdimensional Rift. Along the way, they fight all Exdeath's minions, but are helped by Gilgamesh, who was still alive.
When they find Exdeath, he reveals his true form and proceeds to kill all of their friends, then unleashes the Void over them. However, the spirits of the four Warriors of Dawn appear and hold the power of the Void, so that Bartz can fight Exdeath. Exdeath is defeated, but then he loses control over the Void, which consumes him. He becomes one with the Void, threatening to destroy all existence, but is defeated again. With the Void controlled, the world starts to regenerate, and the heroes are sent back home.