Spoiler warning: Plot and/or ending details follow.
- The Lunarians, a race living on the Moon, have an enormous debate about the people of the Earth. One side, led by a man named KluYa, believed that the Earth was a generally good place, whereas the other side, led by Zemus, believed that it was a corrupted place and deserved to be destroyed. Zemus was overruled, however. In desperation he attempted to destroy the Earth himself, but was overthrown. To vow that such a thing would not happen again, the Lunarians sealed themselves into a deep sleep, appointing only a single Lunarian named FuSoYa (KluYa's brother) to watch over them. The sleep is guarded by eight Crystals.
- KluYa, however, awakens from his sleep, gazes on the earth, and falls in love with an Earth woman. He decides to forsake his race and travel there. He fathers two sons, Cecil and Golbez.
- KluYa dies before his time. His sons are orphaned. Cecil is taken in by the king of Baron and raised as his own.
- Zemus' dormant spirit awakens and tries to awaken his body. To do so he needs the four Crystals of the overworld and four of the underworld, to counteract the eight Lunarian Crystals.
- Zemus takes control of Golbez and turns him into an evil pawn. Golbez gathers four demons known as Emperors: Milon, Cagnazzo, Valvalis, and Rubicant to help him. Cagnazzo in particular secretly kills the king of Baron and assumes his identity. He appoints a demon named Baigan to be his right-hand man.
- Cecil excels in the Dark Sword techniques and rises in the ranks of Baron. His best friend, Kain, is better at the Dragon Knight skills, despite his king's urging to be a Dark Knight as well. Cecil is finally promoted to captain of the Red Wings, Baron's elite airship fleet, created by an engineer named Cid. Cecil also falls in love with a White Mage from Baron named Rosa.
- Having honed the Red Wings' power, Cagnazzo as the king of Baron orders Cecil to steal the Water Crystal from the people of Mysidia, a town of magicians, and destroy any resistance. Expecting war, Cecil prepares for war, only to find a town of unresisting villagers. He takes the Water Crystal, but has doubts about his king.
- Upon reaching Baron, he delivers the Water Crystal, but Baigan senses his wavering and reports to Cagnazzo. Cagnazzo decides to get Cecil out of his way and get rid of a thorn in his side at the same time. He demotes Cecil from the Red Wings, then sends him and Kain to Mist, a village of Summoners, with a bomb disguised as a package. He intends to destroy the summoners once and for all. While Cecil is gone, Cagnazzo invites Golbez in to take control of the Red Wings.
- Cecil and Kain travel through the Mist Cave, but a white dragon stops them. They kill the dragon. Upon entering Mist, however, they are surprised when the bomb goes off and sets fire to the entire village. They come upon a girl weeping over the corpse of her mother; she tells them that her mother's dragon was killed, so due to her link with it she died as well. Cecil realizes the enormity of his deeds and attempts to take the girl with him, but she refuses. He tries to take her by force, but she casts a summon spell in defense. When Cecil awakes, Kain is gone and the girl is next to him.
- Kain is taken by Golbez and brainwashed into being his servant.
- Cecil takes the girl to the oasis town of Kaipo, where he takes the unconscious girl to the inn. In the night, however, Baron soldiers arrive looking for her. Cecil slays them and the girl finally trusts him, giving her name as Rydia. The next day, Cecil finds Rosa sick in bed in one of the houses in town. She arrived here looking for him. The old man caring for her tells him that only the Light of the Desert, found in Damcyan, can cure her. Cecil and Rydia go off to look for it.
- They take an Waterways of Baron leading to Damcyan. On the way they come across an old man named Tellah. Tellah's a powerful sage, but can't remember most of his magic. He's also trying to get to Damcyan; his daughter Anna has eloped with a bard named Gilbert, whom he completely disapproves of. However, the way is guarded by a large Octomammoth. Teaming up, Tellah, Cecil, and Rydia get past it to Damcyan.
- Before being able to enter the castle, however, it's strafed by the Red Wings, who steal the Fire Crystal held there. They go inside to discover Anna dying of her wounds. Tellah goes berserk and attacks the bard, who's actually the prince of Damcyan. Cecil stops him, but Tellah leaves on his own quest to search for the ultimate magic spell, Meteo, determined to kill Golbez for the death of his daughter. Gilbert agrees to take Cecil to the Antlion's Lair, which is where the Light of the Desert resides. He lends him the royal Hovercraft to get over the rocky shoals blocking the way.
- They find the Antlion, but it attacks them before they can get the Desert Light from its lair. They defeat it and return to Kaipo, where they revive Rosa. Rosa tells them that Golbez is after the four Crystals; they decide that the Wind Crystal in Fabul would be Golbez's next target. Rosa joins them as they travel there.
- They pass through Mt. Hobs to get to Fabul. On the way they find a monk named Yang beset by monsters. They rescue him and he introduces himself as a member of the Fabul monks. They hurry to Fabul to fight the onslaught Golbez launches their way. They defeat the monsters, but Kain unexpectedly shows up to fight Cecil. He takes the Wind Crystal and returns to Golbez.
- Yang joins Cecil and crew in their fight against Golbez. Cecil and friends take a ship in an attempt to return to Baron, but on the way they are attacked by Leviathan, a huge Phantom Beast. The crew is scattered.
- Rydia is taken to the land of the Phantom Beasts, where she is welcome, being a Summoner. Leviathan, king of the Beasts, takes her under his wing. Due to the magical field there, Rydia ages rapidly, becoming a young woman far faster than usual.
- Yang lands near Baron and is also brainwashed by Golbez, who turns him into a palace guard.
- Gilbert lands near the city of Troia, badly wounded. The citizens of Troia tend to him.
- Rosa is captured by Golbez and taken to the Tower of Zot, a skybound tower where Valvalis resides.
- Cecil lands near Mysidia, where everyone is frightened of him. He manages to get the elder of Mysidia to semi-trust him, but not quite enough. The elder says that a Dark Knight cannot defeat Golbez; Cecil must attempt to become a Paladin through the trials on Mount Ordeals. He appoints a pair of twins, Palom and Porom, to accompany him and to spy on him as well. Palom is a male Black Mage, Porom a female White Mage, both ten years old.
- Cecil meets up with Tellah on Mount Ordeals. The twins seem to have heard of him. They both journey to the top of the mountain, where they meet Milon. They defeat him, and his undead spirit as well. Cecil continues to the interior of Mt. Ordeals. He meets his own dark side and defeats it by defending. He hears the voice of his father, who grants him the power of the Paladin. Tellah also learns Meteo, and remembers all the spells he had forgotten.
- Returning to Mysidia, the elder grants Cecil travel using the Devil's Road, a magical passage to Baron. Palom and Porom decide to tag along as well. Reaching Baron, they discover the brainwashed Yang, who attacks them. They defeat him quickly, though, and he regains his memories. He finds the key to Baron's waterway on his body, presumably put there when he was captain of the guards.
- They use the waterway to infiltrate the castle. Once inside, Baigan pretends to befriend Cecil, but Palom and Porom see through him and a fight ensues. After winning, they proceed to the throne room where they destroy Cagnazzo. After doing so, they meet Cid, who had his own plans to dethrone the king. They all proceed to Cid's secret hiding place for his last airship, the Enterprise. However, before they get there Cagnazzo's last breath traps them in a room with closing walls. Palom and Porom turn themselves to stone to stop the walls from crushing the others.
- Cecil, Yang, Tellah, and Cid take to the skies on the airship, but are stopped by Kain on a Red Wings airship. Kain tells Cecil that Rosa is in Golbez's power, and proposes a trade - Rosa for the Earth Crystal which resides in Troia. Cecil has no choice but to ask the Clerics of Troia, a female-led city, for the Crystal.
- They travel via airship to Troia, but discover that the Crystal has been stolen by the Dark Elf who lives in the Magnetic Cavern. They also discover Gilbert, wounded. Gilbert gives them an Echo Harp to allow his music to reach them even in far away places. They harness a flying Black Chocobo to reach the Magnetic Cavern, where the strong magnetic field prevents them from equipping metal armor or weapons. Upon reaching the Elf, he immobilizes the party. However, Gilbert's echoing music destroys the barrier and allows them to re-equip their metal weapons and dispatch the Elf. They take the Crystal.
- Kain arrives and brings them to the Tower of Zot. When they finally reach the room where Rosa is held, they are met by Kain and Golbez. Tellah, incensed, uses the ultimate magic Meteo on Golbez, but the stress kills Tellah. Golbez is left largely unharmed, but his control of Kain is broken and Kain joins Cecil and Rosa. Before they can leave, though, they are attacked by Valvalis, the Wind Emperor. After defeating her, they head back to Baron.
- Kain gives Cecil a Magma Stone, which opens the way to the underworld in the town of Agart. Using the airship, they descend the deep hole to reach a dark new world. However, the airship is caught in a battle from the Red Wings. The Enterprise can't travel over the large lava pools underground, so lacking anything else to do they travel to the Dwarf Castle to speak with the king, Giott. Giott tells them that there are four more Crystals underground which Golbez seeks. One is held in the castle.
- Before Cecil and party can take the Crystal, Giott's daughter Luca notices that her dolls have gone berserk inside the Crystal Room; they are being controlled by Golbez. They defeat the dolls, but Golbez's arm appears and steals the Crystal. Golbez himself then shows up to fight Cecil, and summons a dragon. However, the dragon is destroyed by a black magic spell cast by Rydia, who has returned in adult form from the land of the Phantom Beasts. They drive off Golbez. Cid decides to stay behind to help upgrade the airship with mithril found nearby.
- Cecil, Rosa, Rydia, Yang, and Kain attempt a raid on the Tower of Babel, Rubicant's stronghold which stretches from the bottom of the underworld to the overworld. All of Golbez's Crystals are held there. The Dwarves attack the outside of the Tower using tanks while they sneak in. They find Lugae, Rubicant's mad scientist, and defeat him to receive a key to the tower's weapons controls. Yang destroys the controls but locks himself inside to make sure they are not used to attack the dwarves outside. Cecil and party almost manage to escape, but are trapped by Golbez. Cid rescues them in the Enterprise, though, and deposits them in the overworld. He throws a bomb, causing an avalanche and closing the hole to the underworld, trapping himself there.
- Cid's assistants attach a hook to the Enterprise to allow them to take hold of the Hovercraft. They attempt another go at the Tower of Babel through Eblan Cave. There, they see Edge, the ninja prince of Eblan, fighting with Rubicant. He loses, but joins Cecil in attempting the seige. They unexpectedly come upon Edge's parents, though, having been mutated by Lugae. After reluctantly defeating them, Rubicant appears and expresses his apologies for his servant's misbehavior. He heals Cecil before fighting him, and loses.
- Cecil reaches the Crystal Room but is trapped; a hole opens beneath him and his entire party falls through. They uncover an enemy airship and escape on it. Upon returning to the Dwarf Castle, King Giott informs them that the final Crystal is held in the Sealed Cave northwest of the castle. The enemy airship, which can travel over the lava that the Enteprise couldn't, reaches the cave easily. However, right after acquiring it Golbez takes over Kain's mind once more and Kain betrays them yet again, taking the Crystal to his master. With all the Crystals, Golbez's destination is back at the Lunarians' base in the Moon.
- Returning to the Dwarf Castle, Cid is up and about and has affixed a drill nose to the enemy airship, allowing Cecil to drill up to the overworld again. Cecil speaks to the elder of Mysidia, who prays in the Mysidian Tower. Their prayers awaken the Magical Ship, a vessel which can go straight to the moon.
- Cecil meets FuSoYa, who introduces himself and explains everything that happened in the past regarding himself, KluYa, and Zemus. He also tells them of Golbez's plan to activate the ancient Babel Giant, a havoc-wreaking device, to hasten Zemus's plans of destroying Earth. They quickly return to Earth to attempt to fight it.
- They enter the Giant and fight to its control center, but run up against the Four Emperors again. A fierce battle ensues, with Cecil as the winner. Kain arrives with Golbez, but FuSoYa succeeds in breaking Zemus's spell once and for all. Golbez and Kain both regain their consciousnesses. FuSoYa and Golbez go off together to attempt to defeat Zemus, but Cecil is determined to follow them.
- Cecil, Kain, Rydia, Rosa, and Edge speak to the eight Crystals of the Moon, who transport them to the Moon's Core, where Zemus sleeps. They find FuSoYa and Golbez attacking Zemus with Meteo. They succeed in destroying him, but Zemus's alterego of hate, Zeromus, arises from his body. Golbez attempts to use a Crystal to seal Zeromus, but fails because of his alignment with Darkness. He entrusts the Crystal to Cecil. The souls of everyone who helped Cecil from the beginning help him and his party to regain consciousness. Cecil uses the Crystal to reveal Zeromus's true form (rather ugly) and succeeds in defeating it.
- FuSoYa leaves to go back to eternal sleep, but before he can, Golbez asks to go with him. Cecil finally forgives his brother for his sins and tells him to rest in peace. The party returns to Earth. Cecil and Rosa are crowned King and Queen of Baron, and Edge is crowned King of Eblan. Happy ending.
- Cecil can visit the ruins of Eblan Castle and Mist Town for extra treasure.
- A secret room in the Dwarf Castle leads to a place where all the programmers hang out.
- A cave in the underworld leads to the Land of Phantom Beasts. If Rydia and her friends fight Queen Ashura and King Leviathan here, she gains their summons. They can also find a Rat Tail here; if they give it to the midget in the island mine near Mithril Town, it will give them Adamant Ore. Giving that to the dwarf smith Kokkol in the underworld will yield the mighty Excalibur sword!
- A cave in the underworld leads to the land of the Sylphs. Here the party finds Yang, recovering from his wounds in the Tower of Babel, cared for by the Sylphs. They then return to speak to Yang's wife. When they do this, she gives them a Frying Pan to wake Yang up. When they do this, the Sylphs urge Yang to stay. He does, and the Sylphs allow Rydia to summon them. When Cecil returns to Yang's wife and shows her the Frying Pan, she gives him the Cleaver, the strongest throwing dart in the game.
- In the basement of Baron, in the old throne room, sleeps the spirit of the true king of Baron. Defeating it will allow Rydia to summon Odin.
- On the moon is a cave called Hummingway Home, which is full of Namingways, the odd little man in yellow who renames your characters when you talk to him. You can buy special Fat Chocobo Whistles here.
- In a cave on the moon dwells Bahamut, the Phantom Beast God. Defeating him also allows you to summon him.
- In a room in the Moon's Core, there's a very rare chance of meeting dancing Pink Puffs, who have a very rare chance of dropping a Pink Tail. Taking it to the midget in the Adamant mine results in more Adamant being given you, and taking that to Kokkol results in the forging of the Adamant Armor, strongest in the game.
