- The evil Paramecia Empire has an iron grip on the world. A rebel army, led by the king of Fynn, tries to organize a coup against the Empire, but fails time and time again.
- The empire is able to overrun the kingdom of Kas'ion because of the actions of Borghen, its general, who betrayed the kingdom. Gordon and Scott, the princes of Kas'ion, travel to Altair help the king out in his ventures.
- In an attack to attempt to regain Fynn Castle, both the king of Fynn and Scott of Kas'ion are fatally wounded. The king's daughter, Hilda, takes the king to Altair, the rebel base, and takes over in his stead. Scott, unable to escape, is hidden underground by a member of the Rebels.
- Four youths, Firion, Gus, Maria, and Leon, are also fighting against the Empire. They are wounded in battle. Leon is taken by the enemy, but the rebels rescue the other three. They are taken to Altair.
- Leon is brainwashed by the Paramecian Emperor and takes on the persona of a Dark Knight. He is put in charge of the mission to build a giant Warship for the Empire, which is based in the city of Bafsk.
- The three youths decide to search for Maria's brother Leon. Their first stop is Fynn, where the passwords they learned from Hilda gain them access to Scott's deathbed. They take Scott's ring to Hilda, where they learn more of the rebels' plans. Without the legendary metal, Mithril, the rebels have no chance against the Empire. Hilda sends the three youths, along with her magician Mindu (Minu), to Semitt Cave to procure some. Mindu has a canoe which allows them to travel east.
- They travel from the city of Paloom by sea to Poft, and from there via an airship owned by a man named Cid, to reach Semitt Cave. Villagers from the city of Salamand are forced to mine for Mithril here. Two of the miners are Pavel, a thief, and Nellie, the daughter of Josef from Salamand. They are rescued by the three youths and Mindu, who also find a cache of Mithril, which they return to Altair with.
- Hilda now decides to send the youths and Mindu to Bafsk to stop the building of the Warship. When they arrive they overhear rumors that the Dark Knight has been called back to Paramecia, and Borghen has taken his place as overseer of the Warship project. However, Borghen is sloppier than the Dark Knight, and the youths manage to sneak in via the sewers. However, the Dark Knight is waiting for them, and informs them that the Warship is already complete; he and Borghen escape on it. They strafe several cities and kill many people. Gordon escapes to Kas'ion to attempt to retrieve an item called the Sunfire; most think he just ran away. Before leaving Bafsk, the three youths pick up a pass that the Dark Knight leaves behind.
- Cid in Poft tells them that the only way to destroy the Warship is by throwing the Sunfire into its engines. The Flame resides on the lowest floor of Kas'ion. However, to be able to carry the flame they require the Ergil Torch, which itself resides on the highest floor of Kas'ion. To be able to get even there, however, they also require the Goddess Bell to open the door. The Bell is hidden in the Snow Cave to the north.
- Josef of Salamand knows the way to the Snow Cave, but in order to cross the Snow Field they will require the Ice Sled, which is hidden back in Semitt Cave. Josef and the three youths travel there and pick up the Ice Sled. They travel to the Snow Cave. Aided by friendly beavers (whom apparently only Gus can understand) they find the Goddess Bell. However, Borghen the traitor shows up. He is defeated by the party, but causes an avalanche which forces Josef to sacrifice himself to save the others.
- The three youths now travel to Kas'ion, where they meet Gordon, who joins them. Together they collect both the Ergil Torch and the Sunfire. Hilda and Cid arrive in Cid's airship to take you back to Altair, but they are intercepted by the Warship and both Hilda and Cid are taken prisoner.
- The pass left by the Dark Knight gains the three youths and Gordon access to the Warship. They sneak inside, rescue Hilda and Cid, and throw the Sunfire into the Warship's engine, destroying it.
- Back in Altair, the wounded king rewards Gordon by giving him a post in Altair; he also sends the magician Mindu to look for the legendary ultimate magic spell, Ultima. The king sends the three youths to Deist Castle, home of the Dragoons, in hope of gaining their support. The king then passes away.
- The three youths take a ship from Paloom to Deist. However, it turns out to be a pirate ship, led by a woman named Leila. However, the youths defeat the pirates, and Leila joins their quest and lends them her ship.
- In Deist Castle, there are only two survivors, a woman and child. They tell the party that all the Dragoons have been killed, and there is only one dragon (Wind Drake) left. However, no non-Dragoon can understand the Wind Drake without a magical Pendant which is hidden in Deist Cave.
- They find the Pendant. The Wind Drake tells them that it is dying. It mentions that there is one Dragoon named Gareth, who escaped the destruction of Deist when he left to look for Ultima as well. Finally, the Wind Drake asks the party to take its egg to the Spring of Life inside Deist Cave. They do so, and return to Altair.
- On their arrival they discover that Hilda has been captured, and a doppelganger (a Lamia) has been ruling in her place. They dispatch the monster and learn where Hilda is being held: at an Arena, where the Emperor plans on giving her away as a prize to whoever beats the monsters there. Gordon accompanies the youths there while Leila stays in Altair.
- The youths and Gordon beat the monster, but are betrayed by the Emperor and taken prisoner. However, they are rescued by Pavel, the thief, as a reward for rescuing him from Semitt Cave. They regain Hilda and return to Altair, where Gordon stays.
- With the help of Mithril and Leila's pirates, the rebels have organized themselves to be ready to attack the Emperor's stronghold in Fynn Castle. Everyone has moved to a camp near the castle. They succeed in defeating Gotus, the guardsman, and Fynn is retaken.
- Hilda tells them that since Mindu has not returned from his quest for Ultima, they should go to Mysidia to search for him. To do so, though, they need the White Mask hidden in the Fynn Castle Basement. With a hint from Pavel, they find it and head for Mysidia.
- They learn that the Ultima magic is hidden in Mysidia Tower. To enter, they need the Crystal Rod hidden in the Mysidia Cave; to gain access to that, they need the Black Mask hidden in Tropical Island. They collect the mask and rod, and head to the tower, which lies inside a crescent-shaped coral reef.
- Before they can get there, they are swallowed by Leviathan, a sea monster who defends the Ultima spell. Leila disappears. They find an entire village of people swallowed by the monster as they searched for Ultima; included in these is the Dragoon Gareth, who joins them. Eventually they find their ship and escape Leviathan's maw to enter Mysidia Tower. They find four crystal orbs and the Ultima magic inside the tower; Mindu sacrifices himself to break the seal to the Ultima magic.
- When they come out they discover that the Paramecian Emperor has unleashed a whirlwind which destroyed Altair, Gatea, Paloom, and Poft, and Fynn is under attack. Powerful monsters have been unleashed on the world as well. Leila is in Fynn, having gotten out of Leviathan by herself. They discover that the egg from Deist Cave has hatched into a Wind Drake, which flies them to the Whirlwind, where the Emperor hides.
- They manage to reach the Emperor and defeat him, but he has signed a pact with the Devil after which he is allowed to return from death. Before he does so, though, the Dark Knight takes over the Emperor's throne and rules from Paramecia Castle.
- Cid, who was fatally wounded by the Whirlwind, leaves his Airship to the three youths and Gareth. They use it to reach the mountain-bound Paramecia Castle. When they reach the throne room, the newly-resurrected Emperor tries to kill the three youths, Gareth, and the Dark Knight, who reveals his real self as Leon. Gareth Deistracts the emperor long enough for the other four to escape, but is killed for his efforts.
- The emperor changes Paramecia Castle to Pandaemonium, which is connected to Hell. The four youths manage to reach the new castle by going through the magical Jade Portal. They confront the Emperor and defeat him for once and for all.
- South of Kas'ion is a secret forest where a Chocobo lives. If you catch it you can ride it without being accosted by enemies.
- If you visit Gareth's house after he dies, his wife gives you the Excalibur sword.
Soul of Rebirth (GBA/PSP):
- Following the defeat of Emperor Palamecia, the thought-to-be deceased White Wizard Minwu awakens in front of the Jade Passage entrance.
- Upon entering the passage, Minwu sees three Black Knights and man who appears to be Gordon. The two defeat the knights and Minwu discovers that the man is not Gordon at all, but his elder brother Scott. After a brief discourse, Minwu and Scott realize they both had fallen in their efforts against the empire and theorize that they must be in Hell, or perhaps Jade.
- After exploring their surroundings, Minwu and Scott come upon Josef and Borghen, two men also thought to have been killed in the main game's happenings. Speaking about finally having obtained eternal life in this strange place, Borghen attacks Josef and a battle ensues with Minwu and Scott coming to Josef's aid. The battle ends and the three men talk, realizing once again that they all have shared the same fate. Talk of the passage to Hell, Jade, is brought up again, with Minwu hypothesizing that perhaps the reason they are here is that they have some unfinished task left yet to accomplish.
- Descending further into the depths, Minwu, Scott, and Josef come upon a giant worm coveting a chest. Upon approachng it, a voice declares, "Not so fast! This one's mine." A dragoon appears from above, the dragoon citing that the beast had followed him all the way to Hell, and a battle with the Roundworm commences. The four defeat the worm , the dragoon instantly being recognized as Ricard. He informs the rest that Firion and co. were able to claim Ultima but that the Emperor had risen from Hell with hideous power, postulating that it was from this very place that he drew it from. After again coming to the realization that they all died facing the empire and that they are in the passsageway to the location that the Emperor aquired his power from, they put the pieces together that perhaps their meeting here is no coincidence.
- The four finally come upon what looks to be a makeshift town in the middle of Hell. Entering the pub, Minwu spots Cid. Cid explains that this place was just how one would picture Hell, with monsters feeding on anyone they could catch. By the time they found a haven free of monsters to build the town, many had already perished. Cid, however, refutes the idea that the place is actually Jade, asking why innocent children would reside here.
- Coming upon a seal just like the one that Minwu sacrificed his life for prior, Minwu casts a massive spell on it. This time merely fainting instead of dying, Minwu determines that since he died in life, it is his destiny to wield Ultima this time to put a stop to whatever machinations are going on here.
- The group finally comes upon the chamber of the crystals. Upon touching them, each bestow upon them their gifts (in the form of stat increases). When they touch the final, center crystal, Ultima Weapon appears to challenge the party for the right to bear Ultima. After defeating the beast, Ultima Weapon bestows the legendary spell upon Minwu.
- After entering a portal in Machanon, the party comes upon a castle they take to be Pandaemonium. Ascending to he final floor, they come upon the Emperor. The Emperor explains that after being defeated by Firion, he split into his light and dark halves, his dark side plummeting into Hell to become the master of Pandemonium. Surprised, Mindu asks if this isn't Hell. The Emperor continues, saying that the passage they thought was Jade was actually Raqia and that they now stand in Arubboth, palace of the heavens. Having become lord of Arubboth, the Emperor asks them for forgiveness, and would in return give them eternal life in this realm. Not ones to so easily forget the injustices commited by the Emperor and following a scene flashing back to important people in their lives, the party engages the Light Emperor in battle.
- After defeating the Light Emperor, the scene shifts to Firion and the rest of the party defeating the Dark Emperor with Minwu, Scott, Josef, and Ricard watching over them as celestial entities. The scene and the dungeon end with their souls putting faith and hope into the hands of their living allies, hoping that they can reverse the legacy of violence that they tried so hard to stop.