1000 Years Ago:

• Enuo, an ancient evil, creates a "Void" which threatens destruction of the world. The people of the world succeed in defeating Enuo using twelve legendary weapons, but cannot destroy the Void. In desperation, they call upon the power of four Elemental Crystals, which they split in two. The split causes the world to split into two distinct worlds as well, and the Void is trapped in the Interdimensional Rift between the two worlds.
• The twelve legendary weapons are sealed in Castle Kuza in the Second World. Information on how to retrieve them (should the need arise) is hidden in a Sealed Tome, but the book itself is torn in two when the worlds are separated.

30 Years Ago:

• An evil tree awakes in the forest of Moore in the Second World and takes on the form of a dark knight named Exdeath, who begins wreaking havoc on the world. He travels to another world (the First World) and begins trying to destroy the four Crystals there. Four Warriors of the Dawn (Galuf Halm Baldesion, Xezat Matias Surgate, Kelger Vlondett, and Dorgann Klauser) defeat Exdeath and seal him in the First World using the power of the Crystals.
  Dorgann, overcome with regret over throwing their problem to another world, stays with Exdeath in the new world. He settles down in the village of Rix, marries a woman named Stella, and has a son named Bartz. He and Stella both die of illness in the same year.
• On the First World, King Alexander Highwind Tycoon marries and has two daughters, Lenna and Sarisa. However, Sarisa is taken by pirates and raised as one of them, taking the name Faris. She befriends a water dragon named Syldra, who helps tow her ship around when wind is low.
• Queen Tycoon becomes deathly ill. The only cure for her is the tongue of a Dragon, an endangered species. Tycoon's daughter, Lenna, despite her love for the Dragons, resolves to kill it to save her mother, but her father stops her, and his wife passes away.

Present:

• Exdeath begins to stir. He begins to control creatures and people with his mind, with the intent of freeing himself. His first attack is on the Wind Crystal, kept in the Wind Shrine near Tycoon Castle.
• King Tycoon, sensing the weakening of the wind, boards a Dragon to travel to the Wind Shrine. The Crystal shatters, knocking him out, and Exdeath takes control of him.
• Bartz begins a journey with his pet Chocobo, Boko, to see the world, based on his father's dying wish.
• Galuf, king of the Castle of Bal, discovers Exdeath's intentions and boards a meteor to the First World. However, the impact causes him to lose all memory.
• Cid Previa, creator of the Fire-Powered Ship which runs on the Fire Crystal's power, observes the weakening of the Crystal. He begs the Queen of Karnak to stop using the ship and otherwise using the Crystal's power. She refuses, but Cid attempts to shut off the machine himself; she throws Cid in jail.
• Scholars from the Library of the Ancients west of Karnak (where Cid's grandson Mid studies) begin visiting the Queen urging her to stop using the Crystal. She builds a wall west of the town keeping them out.
• Mid descends to the depths of the basement of the Library of the Ancients to look for a method of having the Fire-Powered Ship work on its own. He loses track of time, oblivious of the nearby monsters.
• Lenna begins to search for her father and ends up near Galuf's meteor. She is attacked by goblins, but saved by Bartz. They meet Galuf, who remembers nothing but his desire to go to the Wind Shrine. He and Lenna go there together. Bartz follows behind.
• Bartz rescues Lenna and Galuf from more goblins in a narrow pass; they decide to continue to the Wind Shrine together.
• The fall of the meteor has blocked the way back to Tycoon Castle, but it has also formed a new cave. The cave leads to the pirates' lair. They leave Boko at the entrance (he is later injured, and is cared for by one of the pirates' men). Bartz and co. decide to steal the pirate ship, but are caught by Faris before they can. Faris puts the three in the brig, but a pendant worn by Lenna leaves her to wonder about her own, identical pendant. She decides to join them and take them to the Wind Shrine.
• They find the Wind Crystal shattered. An image of King Tycoon appears to them and describes (vaguely) the situation involving Exdeath and the Crystals. They are shown to be the four "legendary warriors" and vow to protect the other three Crystals. The Water Crystal in Walse is next on their list.
• They travel to the city of Tule. The pirates stay in the bar here. Lenna takes the party to a man named Zok, who has the key to the Torna Canal, which leads to Walse. Zok is at first reluctant to give Lenna the key, but reconsiders when he sees her determination to succeed. He gives the key to Bartz in the middle of the night.
• Inside the Torna Canal, the ship is confronted by a giant sea monster. It creates a whirlpool which sucks Syldra inside. Without any way of steering the ship, it drifts until it reaches a place called the Ship Graveyard, where several wreckages lie. When they find a safe place to rest and dry off, Bartz, Galuf, and Lenna discover that Faris is actually a girl. Before they can leave the Ship Graveyard, they are presented with mirages (Bartz with his mother, Lenna and Faris with King Tycoon, and Galuf with his granddaughter Krile) which puts them in a trance. However, Galuf doesn't remember Krile, breaks off the trance, frees his friends, and defeats the Siren who caused the hypnosis.
• They come to the city of Carwen, where they decide that with their sea transportation gone, they need air transportation. They travel to the North Mountain, where a plant called Dragon Grass grows. It's a cure-all for Dragons, and they figure it's possible that Hiryu, King Tycoon's Wind Drake might have gone there.
• They find Hiryu at the North Mountain. Lenna risks her own life to get the Dragon Grass, walking through poisonous plants to reach it, and in thanks Hiryu heals Lenna and allows all four of them to ride him.
• Hiryu takes them to Walse Castle. Lenna implores the king to stop using the Water Crystal to power the city, but the king refuses.
• A member of Galuf's army from the Castle of Bal arrives via meteor to protect the Water Crystal from a woolly mammoth named Garula, who has recently fallen under Exdeath's control. Another meteor arrives in Karnak bearing a werewolf from Kelger's army to do the same for the Fire Crystal.
• The king of Walse goes to Walse Tower to investigate the meteor and the Water Crystal, but is attacked and wounded by Garula. Galuf meets the warrior but does not recognize him. They defeat Garula, but are not in time to save the Water Crystal, which breaks, or the warrior, who dies.
• A soldier from Karnak wanders into the Karnak meteor and is warped to the Walse meteor. Bartz and party get the hint and take the warp to Karnak.
• Bartz and party are seen coming out of the Karnak meteor and are believed to be in league with the werewolf, Tzuze, seen on the premises. They are thrown in jail, next to Cid. Cid finally manages to break out of his cell, but ends up back in Bartz's cell! Fortunately, the Karnak Chancellor frees Cid because a crack has been noticed in the Crystal. Cid demands Bartz's party's release as well; the chancellor reluctantly agrees. Karnak Castle is on fire due to the Crystal's overheating.
• Bartz and party rush to the Fire-Powered Ship. Bartz manages to cleanse it of monsters, but finds Queen Karnak, controlled by Exdeath, in the ship as well. He defeats the demon possessing her, but it moves on to a Karnak soldier, who jams the switch on the Crystal, turning the power up to full and shattering it. Tzuze appears and saves Bartz and party from the imminent destruction, but cannot escape himself. Karnak Castle is destroyed by fire. Cid, overcome with depression, adamantly refuses to engineer anything ever again.
• Bartz and party enter the Library of the Ancients and look for Mid in the basement. They find him and he shows them the plans he found for restarting the Fire-Powered Ship. Mid travels to Karnak to whack Cid out of his depression (literally). Back on board the Fire-Powered Ship, which is quickly rehabilitated, the scene with Cid and Mid reminds Galuf of a similar scene between him and his granddaughter Krile, and he regains his memory. He explains the entire situation to Bartz, Lenna, and Faris.
• Resolving to protect the Earth Crystal, Bartz and party visit Crescent Town, only to have the Fire-Powered Ship sunk in a whirlpool! They find a flying Black Chocobo in a nearby forest, though. Returning to the Library of the Ancients, Cid and Mid tell them that King Tycoon has been sighted in Karnak, then went southwest through the Desert of Shifting Sands. Bartz and co. follow him.
• The shifting sands of the desert confound Bartz, but Cid calls a sandworm and Bartz walks over its body across the sand. They enter Gohn, the Town of Ruin, a Ronkan relic. They run after the spectre of King Tycoon, but are trapped in a pit and fall down into a strange mechanistic place, the Airship Base. They are carried to just west of Crescent Island, where Cid and Mid have returned the Black Chocobo to its home.
• A switch in the Airship Base ends up swallowing Cid and Mid, where they land on an ancient airship! They meet up with Bartz and, using parts from the Fire Ship, which also ended up here, patch up the airship so Bartz can use it. Before he can go anywhere, though, a huge flying castle arises from Gohn. Cid tells Bartz that the Earth Crystal must be inside. However, without a metal called Adamantite, the airship can't fly that high.
• Galuf collects some Adamantite from the meteor he arrived in, and Cid enhances the airship's capabilities. Bartz and party get past the defenses and enter the flying Ronkan Ruins. They come across King Tycoon again, but he, under Exdeath's control, ends up shattering the Crystal. He threatens to kill Bartz, but another meteor suddenly arrives and Krile knocks out the king before he can do anything.
• King Tycoon comes to, but Exdeath arrives immediately after the Crystal shattes. Exdeath disappears and returns to the Second World, but uses the Crystal shards to attack everyone in the room. Tycoon manages to defeat the shards, but is fatally wounded. Bartz and party barely manage to escape aboard the airship.
• Krile and Galuf use Krile's meteor (the last functioning one) to return to the Second World. Bartz, Faris, and Lenna resolve to follow him to help defeat Exdeath. They return to Cid and Mid (who are at the Tycoon meteor) to ask them for their help in reaching the Second World. They discover that Adamantite can power a meteor, but there isn't enough to power up one meteor completely. Instead, Bartz and co. travel to all four meteors to power them up as much as they can, and create a warp point at center of their four locations.
• Galuf and Krile waste no time in mounting an attack against Exdeath at the Big Bridge near his castle in the Second World.
• Bartz and co. enter the warp and end up on a small island in the Second World, but they are abducted by Exdeath and taken to prison. Exdeath shows Galuf an image of the three and tells him they'll be killed if he doesn't step down. Galuf agrees. Exdeath appoints his right-hand man Gilgamesh to watch over the prisoners and leaves.
• Galuf uses Krile's pet Wind Drake to rescue Bartz and co. He is stopped by Gilgamesh, who is a complete wimp, and who runs away after the battle.
• They reach the Big Bridge, which is under attack by Exdeath's forces. They again are stopped by Gilgamesh, who is aided by his sidekick Enkidu, but he again runs away. However, Exdeath activates a barrier around his castle, which flings Bartz, Faris, Lenna, and Galuf far to the north, to the barren continent of Gloceana.
• They pass the town of Regole and Kuza Castle (the twelve ultimate weapons held within are magically sealed) and enter a forest where they find a moogle. The moogle falls through a pit into the Moogle Canal, which is infested with Moogle-eating monsters! They rescue the Moogle and follow it to its home in the Moogle Forest. The Moogles here communicate telepathically with Krile's pet Moogle, and she quickly rushes to the Moogle Forest to rescue her grandfather and friends.
• Upon returning to the Castle of Bal, Bartz discovers that the Wind Drake that saved him is now dying from its wounds. Again, Dragon Grass is needed, but it only grows in Drakenvale, which lies past the village of Quelb, Kelger's werewolf village.
• In Quelb, the north gate is locked, so they meet up with Kelger. Galuf tells Kelger the other three are from the First World, and Kelger assumes they were the ones who released Exdeath. He ends up challenging Bartz to a duel, which he promptly loses. They also discover that he is Dorgann's son.
• Bartz and co. continue to Drakenvale, where they discover a monster plant, which they surmise must have been the reason for the virtual extinction of the Wind Drake. They retrieve the Dragon Grass and return to the Castle of Bal. The gate guards don't believe that it's really Galuf, so they're forced to use the moat to enter. Krile, who has fallen sick, tells Galuf to seek out the guidance of Sage Ghido.
• They try to get the Wind Drake to eat the Dragon Grass, but it refuses. Lenna shows it that it's not dangerous by taking a bite herself (despite the fact that it's poisonous to humans). The Wind Drake eats the medicine, but Lenna requires her own medicine after that stunt; the Wind Drake heals her again.
• They reach Ghido's island on the Wind Drake, but Exdeath sinks the island before they can enter.
• Returning to Kelger, he tells you that Xezat Matias Surgate, king of Surgate Castle, has assembled a fleet to attack one of Exdeath's barrier towers. The team hurries to the fleet's location near Exdeath's Castle.
• Xezat's fleet is attacked by Exdeath's forces, led by Gilgamesh, but they are defeated. Gilgamesh attempts to pull Bartz into the sea, but Bartz is saved by the Wind Drake. Xezat and Bartz's party head into the Barrier Tower via submarine.
• Xezat heads to the power room while Bartz goes to the antenna on the roof. Xezat gives them a Whisperweed (like a walkie-talkie) to allow them to converse. They reach the antenna and defeat Atomos, the guardian of it. They destroy the antenna and Xezat deactivates the power, but is trapped in the power room. The Shield Generator is destroyed and Bartz and party manage to escape, but Xezat perishes in the power room.
• Ghido's island has sunk into the sea, so Bartz uses Xezat's submarine to reach him. Ghido tells them that Exdeath is searching for something in Moore Forest, and gives them the Guardian Branch which allows them to enter it.
• Exdeath cannot enter the Moore Forest himself, but allows Bartz to open the way using the Guardian Branch, and, being attacked by the Crystals' seals, to destroy them. In gratitude, Exdeath sics the Crystals' power on Bartz and co. Krile arrives but is unable to do anything. Galuf, however, shakes off the trap, shattering one of the Crystals, and begins attacking Exdeath despite the huge energy being thrown at him. He succeeds in driving Exdeath off, but is killed in the attempt. He lends Krile his powers to fight with Bartz instead of him.
• Bartz and co. enter Exdeath's castle. They are confronted by Gilgamesh, who transforms into an eight-armed demon and attacks with the Excalipoor sword, but it's useless. They defeat him and Exdeath banishes him to the Interdimensional Rift for incompetence. The party attacks Exdeath, but before they can kill him the Crystals shatter and the two worlds merge back into one.
• Among other things, Cid is trapped in the Airship Base when the Fork Tower appears above it.
• Exdeath transforms himself into several slivers of wood and hides in an antlion's cave.
• Bartz and group end up near Tycoon Castle. They enter, and the two princesses are warmly received. Bartz and Krile decide to head off alone to defeat Exdeath, and leave the castle. They decide to head to the Pirate Cave (a new bridge has been completed leading there) and see if Boko is still around. They find Boko and a female Chocobo named Koko, whom Boko's apparently married. Boko leaves Koko for the moment and travels with Bartz and Krile.
• Boko, Bartz, and Krile fall into the antlion's cave on the way north, but are rescued (after some toying) by Faris, who rejoins them. Exdeath makes Krile "prick herself" on the slivers of wood containing himself, and thus is carried along with them.
• Bartz and co. find Ghido in a cave, who fills them in on the details of the merging of the worlds. However, Exdeath emerges and declares his interest in capturing the power of the Void for himself. As a demonstration, he pulls Tycoon Castle into the Interdimensional Rift, and throws Bartz, Krile, Faris, Boko, and Ghido far away to a spot near the Library of the Ancients.
• The Sealed Tome has been re-constituted as a whole in the Library of Ancients, and it gives hints to four places to travel to; each place holds a tablet which is the key to three of the legendary weapons. Bartz takes it and travels to the nearby Great Pyramid in the desert.
• They retrieve the tablet, and having done so are visited by the king of dragons, Bahamut, who tells them he will wait in the North Mountain.
• Passing through the remains of the Forest of Moore on the way back to the Library of the Ancients, they are visited by Hiryu, who drops an unconscious Lenna at their feet. However, Lenna is possessed by a monster from the Interdimensional Rift, and attacks Bartz. Hiryu sacrifices itself to save Lenna, though, and the monster is driven from her body and destroyed by Bartz and co. Lenna re-joins, but can't stop Exdeath from pulling the Library of the Ancients, Walse, Istory, the Moogle Village, and Rix into the Void.
• Bartz and co. find their airship again and use it to reach the next tablet location, the Island Shrine, and the Fork Tower, which has appeared above the Airship Base and contains the two ultimate white and black magics. After finding the magics, Fork Tower disappears and Cid is freed. Cid has found a book describing how to transform an airship into a submarine, and effects the upgrade immediately.
• The submarine takes them to the Great Sea Trench, an underwater cave which contains the third tablet and the Meteor spell.
• The fourth tablet and the Leviathan Summon spell are located in Istory Falls.
• Bartz and co. enter the Interdimensional Rift, where they come across Gilgamesh once again. They defeat him and earn his praise and friendship. In another, later battle, Gilgamesh comes to their aid by sacrificing himself to kill the enemy.
• They encounter Exdeath, who transforms into a giant tree. Before they can destroy him, Exdeath is consumed by the Void, transforming into Neo Exdeath, an embodiment of the Void, whose only desire is to reduce everything to nothingness. They manage to defeat him, the towns and castles swallowed by the Void are returned to their former places, and everyone is happy.

Side Quests:

• Shiva lives in the basement of Walse Castle and will allow you to summon her if you defeat her. Same goes for Ifrit in the Library of the Ancients, Ramuh in the forest around Istory, Shoat in a forested area in the Second World, Odin in the the Castle of Bal basement, and Bahamut in the North Mountain.
• There's a Magic Lamp in Istory Falls which allows you to cast free Summons in battle, with weakining intensity unless you recharge it back at the falls.
• Syldra's spirit returns to the Pirates' Cave and will allow you to summon her.
• The Phantom Village is hidden in the forest near Crescent Town. Besides for excellent shops, a Black Chocobo resides here.
• Walse Tower is submerged in water, and a single Crystal shard lies here, guarded by Gogo, the Mimic, who challenges you to a battle. Gogo does nothing in battle, so mimicing him by doing nothing will get you the shard, which teaches the Mimic class.
• Phoenix Tower is located in the middle of a huge desert. At the top you will meet Hiryu, who sacrifices himself to Lenna by diving off the tower and transforming into the Phoenix, who allows you to summon him later.
• In the Town of Moore is a hidden old man who offers you the choice between the Chicken Knife (gains power the more fights you run away from) or the Brave Blade (loses power when you run away).
• In a cave underwater dwells a mysterious old man, Mr. Clio, who'll report on your battle statistics and treasure chest count.
• Two insanely difficult enemies, Shinryu and Omega, are in the Interdimensional Rift; they're quite a bit harder than the final boss!

Side Quests (GBA Version Only)

• After getting all twelve Legendary Weapons, a scholar will come up and tell you than an earthquake was heard to the south. Going underwater there reveals a white rift. Going inside nets you three more job shards - Cannoneer, Gladiator, and Oracle.
• After beating the game, returning to the same place opens the way to the secret dungeon, the Sealed Temple. This enormous area consists of a very high encounter rate, extremely difficult enemies, and a slough of treasure. Among other things, you can fight versions of Omega and Shinryu which make the originals look like jokes (there's a room with no less than five Omegas in it!). At the very end you'll come up against the one and only Enuo, the ancient creator of the Void. Beating him nets you the Necromancer job.
• After getting Necromancer, you will have access to the Cloister of the Dead. This consists of six rooms, each of which require you to fight five boss battles one after another. Beating it gets you a shiny Medal of Smiting.