1000 Years Ago:

• Three godesses or Magi (Doom, Poltergeist, and The Goddess) wage a magical war on each other. Chaos ensues. Any unlucky humans caught in the midst of the huge magical energy are transformed into Espers, magical beasts. Eventually realizing the horror of their actions, the Goddesses seal themselves up in stone statues, taking with them all the magical power they used. The statues are placed inside Crescent Island.
• Eventually it is discovered that the Espers have their own magical power which could be drained from them. Fearing persecution and annihilation at the hands of humans, the Espers create their own dimension and seal the gate.

30 (or so) Years Ago to Present:

• Madonna Branford, a human girl, loses her way and falls into the Espers' world, where she is taken in by an Esper named Maduin. They fall in love and eventually a baby is born, whom they name Terra.
• Gestahl, leader of the Empire, discovers the location of the Espers' gate and breaks through, capturing all the Espers he finds. The elder of the Espers manages to re-seal the gate and banish the humans, but Madonna and Terra also fall through. Madonna naively asks Gestahl to care for Terra; Gestahl takes the baby and leaves Madonna to die.
• Experiments on the Espers by Cid, the resident Empire scientist, leads to the creation of MagiTek, a combination of magic and science. One experiment involving Magitek is tested on Kefka, one of Gestahl's generals. The experiment is successful and Kefka is given magical powers, but his brain is warped by the energy and he becomes a madman. Further experimentation yields a more stable magical infusion (though not as powerful) which is used to create Magitek Knights, humans infused with Esper magic. One of these generals is Celes Chere, who was more or less raised by Cid.
• Terra, whose powers eclipse even Kefka's, is brainwashed and used to carry out military conquests.
• The king of Figaro dies and is succeeded by his son Edgar. Edgar's twin brother Sabin, convinced that the king was poisoned by the Empire, expresses his desire to leave and study martial arts under the teachings of Duncan, a master of fighting. Edgar agrees to a coin toss, which if Sabin wins he would get his wish. Unbeknownst to Sabin, though, Edgar uses a two-headed coin, however, to be assured of Sabin's winning the toss. Sabin trains under Duncan along with Vargas, Duncan's son. Duncan later disappears and is believed to have died.
• Two highway bandits named Baram and Clyde are captured after a huge train heist. Baram is left heavily injured (despite his pleading to Clyde to kill him), but Clyde finds his way to Thamasa, where he falls in love with a local woman. Overcome with remorse, Clyde eventually loses all emotion and becomes a wandering mercenary, calling himself Shadow. His wife later gives birth to a daughter she calls Relm.
• A thief/treasure hunter named Locke falls in love with Rachel, a girl from Kohlingen. However, while taking her to see a nearby treasure cave, a cave-in is started and Rachel saves Locke only to put herself in danger. An old man nearby, knowing the secrets of certain herbs, keeps Rachel in suspended animation. Locke vows to search the world to find a way to bring Rachel back.
• A debutante gambler named Setzer has an airship race with his close friend, Daryl. However, Daryl's airship, the Falcon, malfunctions and crashes. Setzer restores the Falcon, then buries it and Daryl both in a grave near Kohlingen.
• A man whose wife gives birth to a deformed baby throws it out into the wild Veldt. He later loses his mind and believes that it was all a dream, however.
• A band of dissidents known as the Returners begin operating near Mt. Kolts, led by a man named Banon. Their goal is to overthrow the Empire by any means possible.

Present:

• The brainwashed Terra and two Imperial Soldiers, Biggs and Wedge, are sent to Narshe after rumors that an Esper was found in the Narshe mines. They decimate the guards and reach the Esper, who has a reaction to Terra. Biggs and Wedge are destroyed by the Esper's power. Terra is later found unconscious by Arvis, a Returner living in Narshe, who helps her escape. She is later helped as well by Locke, a treasure hunter/thief also working for the Returners, and a gang of Moogles living in the Narshe caves.
• Locke and Terra make their way to Figaro Castle, where she is introduced to King Edgar. Edgar and Locke decide to take her to Banon in the Returner HQ. Before they can leave, though, they are visited by Kefka, sent by Gestahl to retrieve Terra. Kefka first tries diplomacy, then attacks the castle. However, through advanced technology the entire castle sinks under the sands, and Edgar, Locke, and Terra escape by riding Chocobos. They are attacked by Magitek Armor, but Terra wards them off using magic. Having never seen magic before, Edgar and Locke are more convinced than ever that Terra can help them.
• They pass through the Figaro Cave to South Figaro, where they catch a glimpse of Shadow. A nearby cabin seems to have many things that remind Edgar of Sabin. They enter Mount Kolts, but are accosted by Vargas, Duncan's son. Sabin shows up to defend his brother. Vargas attacks Sabin, accusing him of stealing his father's favor, which Sabin denies. Vargas is defeated, and Sabin is convinced to continue with Edgar, Locke, and Terra to the Returner HQ.
• An already rich man in Figaro, tempted by even more money, betrays South Figaro to the Empire, who seize it.
• Banon convinces Terra to join the Returners, but before any concrete plans can be made, news arrives that South Figaro has been taken by the Empire. Locke is sent to South Figaro to gather intelligence, and Edgar, Sabin, Terra, and Banon take a raft on the Lethe River towards Narshe.
• They are attacked by a strange octopus named Ultros; Sabin, enraged, jumps into the water after him, but is sucked away by the current, leaving the other three on the raft.
• Terra, Edgar, and Banon make their way through the Narshe caves to Arvis's house.
• Locke steals the uniform of a soldier and finds his way into a secret passage in Figaro. He finds General Celes there, in chains, being tortured; she has apparently rebelled against Gestahl. Locke rescues her and they travel to Narshe through Figaro Cave.
• Sabin lands near a cabin in the middle of nowhere, where he meets Shadow, who joins him for the time being (apparently having nothing else to do). They come across an Imperial Base where they overhear the plans being dealt out by General Leo, an honorable Empire soldier, and Kefka, regarding the seige of Doma Castle. General Leo is called back to Vector (capital of the Empire), leaving Kefka in charge. Kefka poisons the water of Doma, killing everyone in it, even his own men.
• Cyan, faithful retainer to the king of Doma, after repelling Leo's forces, is incensed by the deaths of his king, his wife, and his son. He madly attacks the Imperial Base, and is helped by Sabin and Cyan. They steal sets of Magitek Armor and make their escape. They end up in the Phantom Forest, which leads to the Phantom Train.
• Sabin jumps onto the train despite the warnings of Cyan, who claims that the train takes the deceased to "the other side". They try to find their way off the train, coming across a swordsman claiming to be Siegfried, but actually being a complete wuss. They manage to damage the engine of the train enough for it to leave them off near Baren Falls, but not before Cyan sees his wife and child board the train destined for "the other side".
• Shadow leaves Sabin at Baren Falls. Sabin and Cyan make it down the falls, and land in the Veldt, a wild area filled with beasts of all kinds. They catch a glimpse of a wild boy as they awaken. In a nearby town called Mobliz, they buy meat and entice the boy, named Gau, to help them to Narshe. Gau tells them of a shiny treasure in Crescent Mountain, which ends up being a diving helmet. They use it to swim through the Serpent Trench, an underwater passage which leads to Nikeah. From there it's a short boat ride to Narshe.
• The elder of Narshe finally agrees to help Banon, but only after hearing that Kefka has amassed forces aiming towards recapturing the Esper, which has been moved into the snowy mountain behind Narshe. Finding General Celes and Terra is an added bonus. However, Kefka's troops are defeated by the Returners and Kefka manages to escape.
• Terra meets the Esper for a second time, this time fully in her senses, and the encounter transforms her into a flying pink creature; she soars away as everyone else watches.
• The Returners decide to search for Terra. First they head for Figaro Castle, which submerges and takes them under the sand to the city of Kohlingen. They continue south to the bandit city of Zozo. At the top of Zozo's tallest building they meet an Esper named Ramuh, who watches over Terra's Esper form. He tells them that she will be fine in time, and that there is nothing they can do - except to save others of his kind, held in the Magitek Research Facility in Vector. Ramuh shows them three shards of Magicite, the form Espers turn into when they are deceased, and tells them that the true power of Espers is only available through this form. He then turns himself into Magicite to help them.
• They resolve to go there, but lack transportation. They hear of Setzer's love for Maria, an opera diva, in Jidoor, and resolve to make their way onto his airship and convince him to help them. Discovering that Celes is a dead ringer for Maria, they substitute Celes for Maria in a performance of the opera. The opera is sabotaged by Ultros, but Locke manages to stage a terrific battle and end up with a winning performance: a happy audience, a defeated Ultros, and Maria (aka Celes) abducted by Setzer.
• Celes lets the other Returners on board after the performance. Setzer agrees to a coin toss; heads Celes becomes his wife, tails he helps them reach Vector. Edgar uses a two-headed coin to assure of Setzer's joining them.
• Setzer takes them to the continent of Vector. They find a Returner sympathizer in Vector who stages a violent sickness to allow them to reach the Magitek Research Facility. There, they discover Kefka draining two Espers (Ifrit and Shiva) of their magic powers. Ifrit and Shiva first fight back, but when they see Ramuh's Magicite they also agree to help the Returners and turn themselves into Magicite.
• Celes and the Returners discover six Espers (including Terra's father, Maduin) being worked on in the lab. They, too, turn themselves into Magicite. Cid enters and discovers this fact, but before he can decide what to do with it he is confronted by Kefka. Kefka claims Celes was working for him all along; Celes denies it, but Locke doesn't know what to believe. Celes causes both herself and Kefka to disappear from the room.
• Cid helps the Returners to escape via a mine cart, after pledging his decision to make the Emperor stop his silly war. They are saved by Setzer's Blackjack airship, but attacked once more by Kefka's mechanical cranes. They shake them off and head back to Zozo.
• Terra awakes at the sight of her father, and tells the Returners of her origins. Back in Narshe, Banon and the elder of Narshe decide to send Terra to the sealed gate to the Esper world to ask the Espers for help in defeating the Empire. They do so, but the move is anticipated by Gestahl. Gestahl empties the nearby Imperial Base of soldiers to allow them easy passage.
• While in Narshe, the Returners encounter a Moogle named Mog held by a thief named Lone Wolf. They save him, and he joins them.
• When they reach the gate, Terra turns into an Esper and opens the passage, but is surprised by Kefka. A gang of Espers escapes and go on a rampage, trashing both the Blackjack airship and the city of Vector. They then regroup in a mountain cave near the city of Thamasa.
• The Returners go back to Vector to find it in flames. Emperor Gestahl has apparently had a change of heart and invites the Returners in. He pleads with them to travel to Thamasa, find the Espers, and ask for their apologies. He also tells them that Kefka has been placed in jail for crimes against humanity, due to his conduct with the Doma case.
• General Leo takes Locke and Terra to Albrook, a port town, where they are met by Celes and Shadow, who have been employed by the Empire to help them. Celes refuses to speak to Locke, though.
• They split up; Leo and Celes go alone, and Terra, Locke, and Shadow arrive in Thamasa, a village of descendants from the Mage Warriors of old. The village tries to cover up their use of magic for fear of persecution. They ask a sage named Strago for any information about the Espers, but he has conveniently forgotten everything about them. His daughter, Relm, shows a liking for Shadow's rabid dog, Interceptor.
• A house Relm visits is set on fire, compounded by the Fire Rods kept within. Locke, Terra, and Shadow rescue her, and Strago finally agrees to help them. They travel to the Espers' gathering place near Thamasa, where they see three statues dedicated to the three Magi and with an inscription saying what took place. They are surprised by Ultros, who attacks them. Relm arrives (despite Strago's commands) and saves them by painting a portrait of Ultros, which comes alive and attacks him.
• They find the Espers, who appear hostile. Terra introduces herself to their leader, Yura, and they agree to speak to Leo. They are themselves overcome with remorse over their actions. Everything appears to be going fine until Kefka shows up with Magitek Armor soldiers. He captures all the Espers and changes them into Magicite, then torches the village. Leo tries to stop him, but is tricked when Kefka puts on an illusion of Emperor Gestahl, and Kefka slays him.
• Kefka and Gestahl break the seal on Crescent Mountain, where they find the stone statues containing the Magi. The power of seal causes the entire island to rise into the air.
• The Returners take the Blackjack to the Floating Continent, but are attacked by the Imperial Air Force, as well as Ultros and his friend Chupon, first. After beating them off, they land on the Continent, where they find Shadow. They then come across a huge magical beast named Atma, guarding the statues; then they discover Kefka, Gestahl, and the three Magi.
• Celes also shows up, having followed behind. Kefka tells her all will be forgiven if she kills her friends; she refuses, stabbing Kefka. Kefka recovers, though, and demands that the Magi lend him their power. Gestahl tries to stop him by using magical spells, but the spells are muted by the statues' field. The statues shoot bolts down, one of which strikes Gestahl dead; Kefka throws the body off the island. He then changes the arrangement of the statues, throwing the entire world into chaos. The Returners barely manage to escape with their lives. The airship breaks up as it takes them away, and the entire world changes shape...
• Debris from all over the world gathers near the center and forms a giant tower. Kefka makes his domain at the top of it, shooting Light of Judgment bolts down from it wherever and whenever he likes, destroying whatever he wishes.
• Figaro Castle is attacked by a tentacled beast and forced under the sands with no way of returning to the surface.
• Terra lands near Mobliz; the adults in Mobliz have all perished protecting the children. She becomes a surrogate mother for the children, and realize she has lost her will to fight. Mobliz is periodically attacked by a demon named Phunbaba, whom Terra just barely manages to stave off whenever he arrives.
• Edgar, trying to make his way back to Figaro Castle, changes his name to Gerad and enlists a gang of bandits, convincing them he wants to steal the treasure inside.
• Sabin lands near the city of Tzen, near Albrook. Setzer ends up in Kohlingen, drowning his woes in drink. Gau returns to the Veldt. Mog returns to the caves of Narshe, where he finds that all the other Moogles have perished.
• Locke continues searching the world for a cure for Rachel, and hears of the Phoenix, a magical creature locked in the Phoenix Caves. He travels there to search for it.
• Cyan takes up his domicile in Mount Zozo. Intercepting a carrier pigeon with a letter, he reads it to discover that the soldier (whom he knows has died in Mobliz) is receiving letters from his love, Lola, in Maranda. Cyan pretends to be the soldier and sends flowers and letters to Lola in his stead.
• Shadow continues his travels, but is trapped by a Behemoth in a cave near the Veldt and lies unconscious.
• Relm becomes a famous painter, and is employed by Owzer, a rich man in Jidoor. However, her painting of a starlet is possessed by a demon, and Owzer's entire art gallery of a house is taken over by monsters.
• Strago is hypnotized by the newly formed Cult of Kefka, who have their base in the Fanatics' Tower. He is forced to stay there with them.
• Celes lands on a small, practically deserted island, where she is discovered by Cid. An entire year passes before she awakes. She cares for Cid, feeding him fish. When he finally recovers he shows her a raft he made, telling her to reach the mainland with it. She agrees.
• If Cid does not recover, she throws herself off a nearby cliff in a fit of depression. She survives, however, and finds a seagull nearby with Locke's bandanna tied on it. This gives her the strength to continue, and she finds a letter from Cid telling her where the raft is hidden.
• She lands in Albrook, and heads towards Tzen. A bolt from Kefka's Light of Judgment suddenly strikes the town, and a large house in the middle of town almost collapses with a child inside it. She discovers Sabin holding up the house, rushes inside, saves the child, and makes it out before Sabin collapses.
• Sabin and Celes head to Mobliz, where they find Terra caring for the children. Phunbaba chooses that moment to attack, but ends up knocking out everyone. Terra tells them she can't help them.
• They travel to Nikeah, where they meet Edgar/Gerad, who professes that he has no idea who they are, trying to keep his cover. They follow him through Figaro Cave (where they come across the fake Siegfried again); a side path leads to the basement of Figaro Castle. Edgar, Celes, and Sabin defeat the monster holding the castle hostage, and Figaro castle rises up again and takes them to Kohlingen.
• They find Setzer in Kohlingen and convince him to help them again. He takes them to Daryl's Tomb, where they find Daryl's airship, the Falcon. As soon as they are airborne, they discover one of Cyan's pigeons traveling to Maranda. They trace it to Mount Zozo.
• They find Cyan in Mount Zozo and convince him to join them. He tells them that he has sighted Gau in the Veldt. They collect Gau as well, and enter a nearby cave to find Shadow unconscious; they also find a powerful blade called the Striker. They take him to Thamasa, but before they can ask him to help them he has already left.
• Shadow continues his mercenary travels, this time searching for the enigmatic Striker blade, and hanging around the newly built Coliseum in case anyone came in with it.
• They travel to Jidoor to rescue Owzer and Relm from the hands of the demon possessing Relm's painting. Relm goes with them to the Fanatics' Tower to rescue Strago.
• They return to Mobliz, where the party is finally strong enough to defeat Phunbaba. Seeing their valor, Terra regains her will to fight and goes with them.
• They travel to the Coliseum up north, where they discover the real Siegfried, and Ultros one more time, who now has a job as a receptionist. They bet the Striker in battle and Shadow shows up to claim it, deciding to join them when he loses.
• They enter the Phoenix Caves, where they find Locke and a piece of Magicite. He takes the Magicite to Rachel in Kohlingen; it succeeds in reviving her for a few precious minutes, but that is all. Phoenix allows Locke to use its power.
• After training, the party is finally strong enough to enter Kefka's Tower from the air and challenge him. They defeat the three Magi and Kefka himself. The Tower then collapses; Shadow, deploring his life, chooses to stay with it. Magic disappears from the world after the deaths of the Magi, and Terra becomes a normal human being at last.

Side Quests:

• Sabin finds Duncan still alive, training near Narshe. Duncan teaches him his most powerful technique, the Bum Rush.
• The Esper in Narshe, Tritoch, lends them his power after they defeat him; the way is then opened to a new cave below Narshe. They find a huge Yeti named Umaro there, guarding the Terrato Magicite. Mog forces Umaro to join them.
• A triangular island is home to a huge monster called the Zone Eater, who swallows the party. Traveling inside it, they come across a mimic named Gogo, who joins them as well.
• They discover Gau's father, a crazy old man, near the Veldt. They dress Gau up, teach him manners, and take him to his father, who nevertheless refuses to recognize him. Gau is still happy that his father is alive.
• Cyan takes a rest in Doma Castle, and is attacked by three dream demons, who possess him. The party rescues him from Wrexsoul, a monster who steals people's souls by feeding on their sadness. They purge the demon and release Cyan's pent-up energy.
• A flying monster named Doom Gaze holds the Bahamut Magicite.
• Eight dragons hold the seal to the Crusader Magicite. One of them, the Dirt Dragon, is holding up the performances at the Opera House.
• An old man in Narshe has discovered the Ragnarok Magicite, which he offers to make into a sword or leave as a stone.
• An ancient castle lies beneath the Figaro Desert, and is reached when the castle bumps into it in its trips below the sand. They find the remains of Odin, an Esper king. Taking it into a secret passage downstairs, tears from the statue of Odin's wife transforms the Magicite into Raiden.
• Strago and Relm find Gungho, an old friend, recovering from injuries in Thamasa. He tells Strago that Hidon, a monster they both fought as a youth, has been sighted in Ebot's Rock nearby. Strago and the party travel there and defeat Hidon.