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On the unnamed planet that is the setting for the game, astronomers begin to notice that one of two moons is beginning to glow a reddish color. This revelation occurs in conjunction with increasing numbers of hostile monsters throughout the world. The most powerful nation in the world, the monarchy of Baron, begins utilizing its unparalleled air force (the "Red Wings") and its legions of Dark Knights to attack peaceful nations in search of four Crystals, each corresponding to a different classical element.
Cecil Harvey, leader of the Dark Knights, begins to question the king's motives after forcibly stealing a Crystal from the wizards' town of Mysidia. Upon questioning the king, Cecil is stripped of his rank and sent, along with his friend Kain Highwind, to deliver a package to the village of Mist, which is known for its population of "Callers", wizards capable of summoning powerful monsters. Cecil reaches Mist, only to find that the package is magically rigged to generate a firestorm that would destroy the village. Shocked, Cecil finds a young girl, Rydia, the only survivor of the blaze. Naturally terrified of the Dark Knight, Rydia calls upon a Titan who causes a massive earthquake, altering the landscape.
Cecil recovers from the quake to find Kain gone and Rydia unconscious. Cecil carries Rydia to an oasis where he finds his girlfriend, Rosa, who followed Cecil on his journey but fell ill in the desert. On his search for a cure, Cecil meets an eccentric old wizard named Tellah, who is searching for his eloped daughter. The party reaches the castle of Damcyan just in time to see it obliterated by the Red Wings. Tellah finds his daughter dead and her fiance Edward alive, then leaves to seek revenge. Edward follows Cecil and grants him the usage of a hydrofoil, which leads to a cure for Rosa.
Cecil reaches the nation of Fabul, known for its army of karateKarate or karate-do is a budo art, a Japanese martial art introduced to the Japanese main islands from Okinawa in 1922. Karate emphasises striking techniques (i. punching and kicking) over grappling. Karate training can be divided into three major parts, experts. Since Fabul houses a Crystal, Cecil persuades the king to organize a defense against the impending Red Wings attack. A karate master named Yang speaks on Cecil's behalf as Cecil had saved Yang while journeying to Fabul. During the ensuing battle, Cecil and his friends successfully defend the castle, but lose the Crystal to Kain and Golbez, the new captain of the Red Wings.
Next, a naval assault is planned on Baron, but is thwarted when a Leviathan arises from the depths and swallows the ship carrying Cecil. Alone, Cecil wakes up on a distant shore, which he soon learns is near Mysidia. After persuading the villagers that his intentions are pure, Cecil is sent on a quest to become a Paladin, accompanied by youthful twin wizards who are later revealed to be spies. Cecil travels to Mount Ordeals where his Dark Sword is useless, and unexpectedly completes the quest, literally defeating himself in one-on-one combat. At the top of the mountain, Cecil's party enters a room of mirrors, where Cecil is bestowed power by a mysterious light which refers to Cecil as its son. Tellah also regains his memory on on the spells he had forgotten over the years, as well as the ability to cast Meteo, the ultimate magic. Impressed, the village elder helps Cecil and the twins return to Baron to plan an assault. Invading the castle by using underground tunnels, Cecil defeats the possessed king of Baron, then commandeers an airship with the help of his friend Cid, chief engineer of the Red Wings.
Once on the airship, Cecil is met by an airship commanded by Kain. Rosa has apparently been kidnapped by Golbez, and Kain offers her safe return in exchange for Cecil retrieving the final Crystal, which has been stolen from the picturesque nation of Toroia by the Dark ElfDark elves is the name for the (mostly) evil counterparts of the elves in many mythologies and fantasy settings. They are often at war with other elves. Dark elves in mythology and folklore Norse mythology In Norse mythology, the Svartalfar ( black elves and hidden deep within a magnetic cave where usage of metallic equipment is impossible. The Crystal is found, but Golbez reneges on his promise to return Rosa upon being presented with it. The aging Tellah casts Meteo on Golbez, defeating Golbez but also killing Tellah. Rosa is rescued alive and unhurt, and the previously brainwashed Kain is found ostensibly cured. Kain says that Golbez has not retrieved all of the Crystals; four more, called the Dark Crystals, are hidden in the underground land of the Dwarves, and Golbez has already stolen two of them.
Cecil travels to the underground, but once again fights a failed battle for a Crystal at the Dwarf Castle. Learning of a plot to destroy the Dwarves with a Super Cannon, Cecil travels to the Tower of Bab-il, a huge tower with sections both above and below ground, and through Yang's sacrifice, destroys the Super Cannon, but finds himself trapped in the ensuing chase. Cid sacrifices himself, bombing the passage to the underworld while the party escapes on an airship. Cecil is safe, but for the time being unable to return to the underworld.
The only option for returning is through the Tower of Bab-il. It is discovered that a country near the tower, Eblan, has been destroyed by the devil-like Rubicant and its inhabitants forced underground. A ninja and prince of Eblan, Edge, joins Cecil after a failed attack on Rubicant. The group assaults the tower and defeats Rubicant, but not before Edge watches Dr. Lugae transform his parents into monsters and defeats them in combat. Cecil reaches the stolen crystals, but falls through a trap back to the underworld.
The final Crystal is held in the Sealed Cave, which the apparently unharmed Cid helps Cecil to reach. Cecil retrieves the Crystal, which is lost when Kain once again betrays him. In order to discover what plan Golbez has for the Crystals and hopefully stop it, Cecil travels to the planet's second moon.
On the moon, Cecil learns that he is descended from a race known as Lunarians, who originated on a planet that was destroyed to form an asteroid beltThe asteroid belt is a region of the solar system falling roughly between the planets Mars and Jupiter where the greatest concentration of asteroid orbits can be found. It is termed the main belt when contrasted with other concentrations of minor planets,. The moon is actually a sort of cryogenic spaceship where the Lunarians are held in stasis. Cecil's father was responsible for storing the Crystals, which correspond to Crystals on the moon that hold the thoughts of the Lunarians, on the planet and introducing technological advances such as the airship. However, some Lunarians, led by the evil Zemus, want to wipe out all life on the planet for Lunarian inhabitation. It is revealed that Golbez plans to use the Crystals to revive a giant android, the Giant of Bab-il, and clear the planet for this purpose. Cecil also learns that the light at the top of Mount Ordeals was actually the spirit of his father.
Accompanied by a Lunarian, Fusoya, Cecil returns to the planet to find the Giant revived. However, massive fleets of airships come to distract the Giant, and Cecil sneaks inside. After destroying the Giant's nerve center, Cecil finds Golbez and Kain. Fusoya is able to break the control over Golbez and Kain by Zemus. It is at this point that Cecil finds that Golbez is his brother. Golbez heads to the moon to attempt to defeat Zemus, and Cecil follows.
On the moon, Cecil watches Golbez and Fusoya defeat Zemus, only to find that a more powerful being named Zeromus lay in wait in the aftermath. Golbez and Fusoya are defeated by Zeromus, but Cecil is successful. After Cecil is victorious Golbez (still living!) decides to stay on the moon with FuSoYa because he can't bear to go back to Earth because of his previous actions.
The ending is typical for a Final Fantasy game; the world is at peace, and we are shown, one by one, what has become of the characters in the aftermath. Most notably, Cecil and Rosa are married and crowned King and Queen of Baron.