The story of Final Fantasy VI begins on a mountain top surrounding the city of Narshe. The Empire has learned of a frozen Esper's whereabouts in one of the caves, and has issued an infiltration of the city and it's surrounding mountains. Terra Branford is leading the raid, accompanied by Biggs and Wedge, who are all operating advanced Magitek Armor. Terra is in a coma-like state due to a mind control coronet placed upon her by the Empire so she wouldn't defy orders or flinch at the thought of hurting others in the process of carrying out her orders. The three find the frozen Esper, Valigarmanda inside the Narshean caves. In an attempt to take the Esper back to the Empire's Castle, Valigarmanda kills Biggs and Wedge in their fight, and also destroys the mind control coronet that was placed upon Terra. Due to the sudden dissipation in the mind control, Terra's mind is affected and has temporary amnesia. At this time, the ground beneath Terra collapses, and the Empirean army is fast on her chase in order to bring her back in their hands. Terra manages to escape the army with the help of a thief named Locke Cole, as he vouches to protect her from the Empire until she regains her memories. Locke decides to take Terra to the Returners hideout, who are a group of radicals opposing the Empire and it's march towards Imperialism.
Along the way, Locke and Terra pass through the Kingdom of Figaro, a high tech kingdom in the middle of the desert. In Figaro, Locke introduces Terra to Edgar Roni Figaro, the King, who is a suave ladies man with a lot to say, but is more than capable of backing up his words. Edgar and the kingdom of Figaro plead neutrality with the Empire, but is secretly on the side of the Returners. Terra also learns about Sabin, Edgar's brother. Sabin won a coin toss rigged by Edgar that would decide who would not be inherit their father's thrown. Sabin complies with the outcome and leaves his royal heritage behind in order to become a martial arts expert. It doesn't take long for the Empire to realize that Terra broke free and escaped, and so Kefka and a group of soldiers appear at Figaro castle and demand Edgar hand Terra over. Edgar, not willing to comply, takes Locke and Terra, and the three plan to escape the to the Returners hideout, but not without opposition from Kefka and his fleet first. During their escape, Edgar and Locke discover that Terra is not your ordinary human, and has the power to use Magic. Astonished by this, Edgar suggest that Terra should side with the Returners in order to give them the upper hand against the Empire. After the three retreat towards the Returners home base, the Kingdom of Figaro sinks underneath the sand. Edgar explains that the castle was designed and constructed specifically for sinking purposes, in order to have the advantage during wars and invasions. Along the way they encounter Sabin who was training in the nearby mountain area, and decides to accompany his brother.
At the hideout, Locke introduces everyone to the leader of the Returners, Banon. Banon explains the situation to Terra, and of the Empire's plans for Imperialism. Just as Terra agrees to help out the Returners, the Empire attacks South Figaro, a town leading to their base. Locke heads for South Figaro in an attempt to slow down the Empire's advance, and the rest of Terra's group and Banon head for Narshe, via rafting across the Lethe River, to investigate the frozen Esper in the caves. Along the ride, they encounter Ultros, who gets defeated, however Sabin jumps in the river after him to make sure the enemy is fully killed, however separating himself from the group in the process, leaving Edgar, Terra and Banon alone on their way to Narshe. The scenario then splits into three, and the option is given regarding which portion of the story you want to continue with next, between Locke, Terra, or Sabin's scenario.
During Locke's scenario, he sneaks around the town of South Figaro, who is under heavy military occupation, undetected, in order to slowly jam their communications, in order to buy Terra and the others time. During his raid of the town, he encounters a young woman held hostage. She reveals herself to be Celes Chere, one of the three generals of the Empire. Celes is accused of treason and is therefore imprisoned and interrogated. Locke helps her escape, and the two make their way to Narshe, but not without severely slowing down the Empire in South Figaro first.
Sabin makes his way down the Lethe River and eventually makes it to dry land. He enters a small shack near the river and encounters Shadow, a mercenary ninja. Shadow expresses his dislike towards company and that he doesn't trust anyone, however seeing as he is heading towards the same direction as Sabin, he agrees to temporarily accompany him. Shadow warns him that he may leave at any point he wishes, however. Along the way, Sabin and Shadow have to pass through the Kingdom of Doma. Doma is a Kindgom that is ran by once Samurai and those trained in the art of the blade. General Leo, one of the three commanding generals under Emperor Gestahl, was ordered to take over Doma and use it as a military base. Leo questions his Emperor's orders, however doesn't have it in him to betray him or his nation. Having his emotions get the best of him, Kefka notices this and releaves Leo of his orders in Doma. Sabin and Shadow overhear the conversations between the soldiers about General Leo and his virtue, and even Kefka's plans for Doma's fate. Kefka proceeds by taking full control of the situation and poisons the river surrounding the kingdom of Doma killing all of it's soldiers, inhabitants and King. The lone survivor is a samurai, Cyan Garamonde, who goes insane by the loss of his wife and child, and launches a final stand assault on the Empire and the soldiers outside the castle. Sabin and Shadow notice this, and give him a hand in eliminating a good handful of soldiers before making their escape outside the Empire's reach. The three make their way to Narshe, and Sabin comforts Cyan by revealing to him information about the Returners and their plans to overthrow the Empire. Along the way, Cyan is constantly tormented by the images of his lost family and kingdom, and swears revenge upon Kefka and the Empire. Shadow leaves the group, like he promised to earlier, leaving Sabin and Cyan alone, slowly advancing forward.
The two cross the Veldt, a large plateau, and meet a feral child, Gau. Startled by him at first they ignore him hoping he would leave them alone, but after a few encounters with the child, Cyan suggest that he could be of use, and feels sympathy for him and the fact that he is all alone. Sabin agrees to take Gau with them and eventually meet up with the rest of the group in Narshe, after a long haul through rivers, caves, forests and dodging an imperial raid.
When everyone regroups in Narshe, Locke introduces Celes to the Returners, and Sabin introduces Cyan and Gau. Cyan and Gau have no problem fitting in, however Celes being one of the three generals in the Empire's army has a bit of difficulty earning their trust. One of the Returner members states that they have knowledge of the Empire moving fast towards Narshe in hopes of capturing the frozen Esper in the caves. From that point on, the Returners devise a military strategy in hopes of defeating yet another Empirean fleet and stopping them from reaching the Esper. Kefka leading the assault on Narshe manages to reach the Returners in the mountains, but eventually gets defeated, and he retreats back to the Empire's base. Upon the Returners victory, Terra approaches the frozen Esper, and goes mad in the process, which ports her to transform into an Esper like creature herself. Shocked, scarred and horrified at her new self, Terra flies away in despair, away from Narshe.
The Returners, all confused and shocked as to what they just beared witness to, decide to track down Terra. After heavy searching they get a few clues that lead them to believe she collapsed in the town of Zozo. Locke takes three others with him, while the rest remain in Narshe in order to keep an eye out on the Empire. In Zozo, Locke manages to track down Terra, exhausted and passed out, under the care of the Esper, Ramuh. Ramuh explains that he found Terra fying around uncontrollably until she collapsed from exhaustion. He also reveals to Locke that Terra has Esper blood inside of her, and that if they wish to help her, they need to track down some other Espers that are being held captive at the Magitek Research Facility, in the capital city of the Empire, Vector. The only problem is, Vector is on the southern continent surrounded by water, and the Empire doesn't grant access to commoners. An idea sparks in Locke's mind having heard of the worlds only Airship, and its pilot Setzer Gabbiani. Setzer enjoys being the life of the party and notoriety is his goal. Locke also knows of an Opera House not far from the southern continent in which he is almost positive that Setzer would attempt to crash it, were there a big play in the process.
The Returners make their way to the Opera House from Zozo, and speak to the manager in hopes of putting on the play of a lifetime, with Celes as the lead role. Locke plans on taking advantage of Setzer's predictability and recruit him as a Returner in order to gain access to his Airship so they can make their way towards Vector. Locke is correct in his assumptions, and Setzer comes and tries to kidnap Celes in the middle of the play, but soon finds out that the whole thing was a setup in order to get into contact with him. Locke explains to Setzer how vital it is that he helps them, and Setzer agrees to leave it all on the fate of a coin toss. Celes agrees to marry Setzer if it's tails, and if it's heads, he must help them. Celes uses Edgar's double-sided coin and wins the bet, but not without Setzer catching onto it. Instead of being angry, Setzer is thrilled that Celes would have the brains to pull a fast one, and gladly takes the Returners to the Magitek Research Facility, just outside Vector.
As Locke and Setzer infiltrate the Magitek Research Facility, they discover the horrendous experiments that Dr. Cid has done on Espers upon direct orders from Emperor Gestahl. Locke and Setzer manage to defeat Ifrit and Shiva, and in return obtain a little bit of valuable information regarding the experiments done on them. They then sacrifice themselves and transform into Magicite, giving the Returners pure Magic ability. As Locke advances further, he reaches the main research department and witnesses all the Espers inside test tubes. As Locke tries to free them and take them back to Zozo, they refuse the offer and instead also sacrifice their own lives and transform into Magicite in hopes of giving enough power to the Returners so that they can stop the Empire. One of the Espers sacrificing his life was Maduin, Terra's father. The security alarm triggers, and Kefka makes his way down to the laboratory in an attempt to stop them. Kefka tries to trick the Returners into thinking Celes is a double agent and still working for the Empire. Locke and the Returners partially buy into Kefka's bluff, however an anguished Celes proves her loyalty to him and the Returners faction by opening a secret escape hatchet and forces them to leave, while she holds Kefka and the Empire back. Locke ashamed of doubting Celes tries to hide his emotions as he hopes that she is strong enough to hold her own until he comes back for her.
Setzer hastily takes Locke and the Returners back to Zozo. With the Magicite in their grasp, they are one step closer to bringing Terra back to normal, and stopping the Empire. Locke explains to Ramuh the Espers decision of self sacrifice and presents to him their Magicite. Terra reacts to the Magicite of Maduin, her deceased father, and regains all of her own memories as a child, and that of Maduin's as he tried to prevent Emperor Gestahl and the Empire from invading their homeland.
Eighteen years prior to Terra's birth, Maduin encountered a human woman, Madonna who managed to find her way into the Esper world due to a weakening in the barrier seal. Maduin came in contact with her and decided to take her under his care. The rest of the Espers disapproved, but much to Maduin's surprise, he didn't care. The two had a baby girl, who they called Terra. One day the Empire forced their way into the Esper world, knowing full well that the seal was weak, and attempted to enslave all the Espers in order to strengthen themselves. The Esper Elder sought to put an end to the Emperor Gestahl's assault and cast a spell that drove all past a certain limit, outside their world, however Maduin, his wife, and Terra all got caught in the spell and ended up outside the Esper gate, alongside many others. Emperor Gestahl did not get his wish, however he also didn't go home empty handed. Now with a handful of Espers at his disposal, a half human hybrid, and with knowledge of the Esper world, he retreated and planned his next attack, this time, hoping to come out victorious. As Terra was raised under the Empire's control, she was experimented and tested on constantly and became the Empire's guinea pig.
At this time Terra's flashbacks end, and she is no longer afraid of what she is, and comes to terms with being a half-esper. A newly rejuvenated Terra is now also capable of controlling her powers, and can transform into Esper at will.
At this time, the Returners decide that the Empire has hurt enough people, and plan on launching a full frontal assault on the Empire, with the help of the Espers. The group heads from Zozo to the Returners base in Narshe, and agree that Terra must establish contact with the Esper world, in an attempt to form an alliance and help them carry their assault on the Empire. Terra obliges and manages to get through to the Espers, explaining to them the current situation. When Terra reveals to them that the Espers that were once captured by the Empire, are no more, they become infuriated, and launch their own assault on Vector, destroying the town and much of the Empire's military strength. Emperor Gestahl, appauled at the strength and fury of the Espers, claims that he has had enough with throwing others lives away for the sake of power. Gestahl invites Terra, Locke, and the rest of the Returners to a banquet at the Empire's castle, in hopes of negotiating a peace treaty between the Empire, the Espers, and the rest of the nations the Empire has occupied. Gestahl also apologizes on Kefka's behalf for his war crimes, and imprisons him. After the Empire reaches a conclusion with the Espers, they ask that Terra deliver the contract to them. Terra agrees and is accompanied by Locke, Shadow (whom the Empire has hired), and Generals Leo and Celes. The five individuals head for Thamasa, where the cave leading to the Esper world lies.
Once in Thamasa, the group meet Strago Magus, and his granddaughter, Relm Arrowny, who agree to help situate the group and find the path to the Esper world so that Terra can deliver the peace treaty from Gestahl. Upon arrival to the Esper land, Terra attempts to negotiate with them, however shortly during the process, Kefka launches an attack on the Espers, and kills as many as he can in Thamasa, and taking their Magicite as his own. General Leo, livid at Kefka's dishonor attempts to defend the Espers and engages Kefka into a duel. Kefka makes very quick work of Leo with his newfound Magicite, and kills him as he and Gestahl make their way towards the Esper gate. At this point it becomes clear that the peace treaty was nothing but a ploy in order to get the Esper gate opened for the Empire. Gestahl and Kefka make their way into the Esper land and discover the Warring Triad statues, before the Returners could stop them. Gestahl and Kefka use the powers of the Warring Triads to raise the Esper World above the land, and transform it into the Floating Continent. Amazed at their newfound power, Kefka defies Gestahl, and manages to outsmart and overthrow him with the help of the Triad Satues. The once mighty Emperor, now beaten, falls before Kefka's feet, as Kefka simply pushes his lifeless body off the Floating Continent. Kefka then removes the three statues from their original alignment, causing a disturbance in their magical power which reshapes the world. Earthquakes and natural disasters run wild, as the Returners try to make their way back to Setzers airship and escape, however they are caught in the massive destruction from the magical disturbance, and are all separated from each other. Kefka has won.
One year passes, and Celes awakens on the shores of a deserted island in the care of Dr. Cid. She learns that she was in a coma for this long and that it is uncertain what exists outside the island, as Kefka has been using the power of the Warring Triads to take control over the world, and destroys any faction that opposes him. Plant and animal life is becoming extinct, and diseases plague whatever is left of the world population. Celes, refusing to accept the fact that Kefka has won, sets off the island with the help of a raft Cid has build over the past year, and slowly finds her old comrades one by one. Once Celes comes into contact with Setzer once more, he reveals to her that there is another Airship in the world, who belonged to his now deceased friend Daryl. At this point in time, you have the option to recruit as many of your old allies as you wish, before you deliver the final invasion on Kefka's tower. All the characters are still alive, and should you chose who you want to take, up to a 3 man team of 4 can be utilized inside Kefka's tower to bring him down.
Once Celes, Locke, and Terra manage to each lead their respective group assault on Kefka, they manage to destroy the Warring Triads, only to discover nothing changes. At this point it becomes evident that during his reign, Kefka has managed to fully drain the Statues of their power, becoming the essence of Magic, itself. A reborn Kefka, with God like powers, now opposes the Returners for one final stand. With everything they have, the Returners manage to defeat Kefka once and for all. With the defeat of a God of Magic however, all Magic also dissipates, as each of the Returners Magicite become to shatter, and Kefka's tower begins to collapse. Terra leads everyone outside the tower as she begins to weaken due to her being half-esper, however before Maduin's Magicite shatters, he tells her that she has the power to overcome the Magic disintegration by holding on to her human side. Terra leads the Returners back to Setzer and his airship just in time before the tower collapses.
The story concludes rather ambiguously, but for the better. With Kefka's demise, the world slowly begins to rejuvenate, and a humanity once filled with despair, counting down the last days of their lives, are jolted with a new sense of life. With the Empire and Magic now gone, everyone begins anew, and the Returners each go their own way to live their lives.