Questioning what the second moon could mean, Cecil continues to battle alongside Rosa, and is joined by Cid. The group battles their way to the castle's ramparts, when Cecil, sure that Baron will fall, orders Cid to take Rosa and retreat.
As Cid and Rosa reluctantly agree, Cecil witnesses the Eidolon Bahamut descend from the moon carrying a Mysterious Girl resembling Rydia. Cecil questions her identity, only to be attacked and defeated by Bahamut. Meanwhile, the Red Wings fleet is damaged, Edge and the dwarves witness a strange occurrence involving the Tower of Babil, and the Mysterious Girl enters the Eidolons' realm of Feymarch to claim the powers of Leviathan and Asura.
The Red Wing fleet crash-lands and Ceodore, the sole survivor, resolves to carry out Captain Biggs's final order: to return to Baron. Accosted by monsters, a Hooded Man garbed in robes rescues him, and the two set out for Mysidia, where Porom helps them reach Baron by way of the Devil's Road. They find the kingdom is safe, though the soldiers are acting strangely and refuse to let Ceodore into the castle. Infiltrating the castle through the waterway, Ceodore finds Cid's airship missing and concludes the castle's inhabitants have been supplanted by monster impostors, while the Hooded Man briefly encounters "Cecil".
The two leave the castle and travel through Mist Cave, chased by the impostor soldiers on the king's orders. As the two prepare to traverse the mountains east of Mist Village in hopes of losing their pursuers, the Hooded Man reveals he is searching for a former Dragoon of Baron, vowing to defeat him even at the cost of his own life.
Rydia's Tale: The Eidolons ShackledEdit
Years ago Edge assisted in the rebuilding of Mist, which also received help from Cecil of Baron and Yang of Fabul. Edge had turned to selling Eblan's royal treasures to help fund the reconstruction. Rydia attended Ceodore's birth and before the Mysterious Girl arrived in the Feymarch, Rydia was visiting its Eidolons, but was confronted by Asura who had expressly forbidden Rydia from returning, stating she belonged with her own kind.
Following the Mysterious Girl's attack, Rydia finds the Eidolons petrified. She discovers she is unable to call upon them for aid, and is cornered by monsters while attempting to return to the Underworld, only to be rescued by Luca, daughter of the Dwarven King Giott and Cid's apprentice.
They return to the Dwarven Castle aboard the airship Falcon, and witness the Red Wings airship fleet arrive. Within the castle, they find the Mysterious Girl has claimed three of the Dark Crystals, with only the one kept in the Sealed Cavern remaining. With Giott's permission Rydia and Luca set out for the Sealed Cavern and though they recover the final Dark Crystal, the Mysterious Girl appears and defeats them. She taunts Rydia, destroys Calca and Brina, and takes the Dark Crystal. Rydia and Luca flee the Underworld aboard the Falcon and retreat to Agart for repairs.
They enter a cave and find some of the material they need to fix the Falcon and scrap Calca and Brina for the remaining parts (in an alternate scene, if the player found a Mythril Nut, Mythril Spring, and Mythril Bolt, the Falcon will be completely fixed and Calca and Brina are repaired). Shortly after finishing the repairs, the Eidolon Titan attacks them, but a man clothed in dark armor and a black mantle appears and defeats the phantom creature. The Man in Black boards the Falcon and urges the pair to travel to the Tower of Babil before history repeats itself.
Yang's Tale: The Master of FabulEdit
Yang is training three monks of Fabul. His daughter, Ursula, enters the castle and pleads with him to train her, but he refuses. She goes to Mt. Hobs to train on her own, where she witnesses the Red Wings approaching Fabul. After being attacked by a Mother Bomb and rescued by her father, the pair returns to Fabul where they find the Red Wings attempting to steal the Crystal. The Red Wings are being led by Kain Highwind, who claims to be acting of his own free will.
Following a battle with Yang and his daughter, Kain retrieves the Crystal and departs. Yang and Ursula venture to Baron with the help of three monks, but during their voyage they get stuck on an uncharted island and must find fuel for the ship. Yang and Ursula are separated within a dark forest and the three monks traveling with them are attacked by an Adamantoise, which barely takes any damage from their attacks.
Ursula attempts to rescue them but cannot win. Yang reunites with Ursula, and they band together to defeat the turtle. After they find the fuel for the boat, Yang tells Ursula she has understood something more important than pure strength and allows her to train with him, but asks Ursula to no longer address him as "father", and instead call him "master." They board the ship and resume their course to Baron, but on the way the vessel is swallowed up by Leviathan's whirlpool.
Palom's Tale: the Mage's VoyageEdit
Palom, vowing to follow in the footsteps of the Great Sage, Tellah, had set out for Troia where he trains the young priestess Leonora in the arts of Black Magic. When the Mysterious Girl attacks the city to obtain its Crystal, Leonora opens an underground passageway for them to escape.
Palom and Leonora capture a black chocobo and travel to the Lodestone Cavern. They battle the Dark Elf, but it is defeated by the Eidolon Shiva. Confronted by the Mysterious Girl, Palom takes the Crystal and tells Leonora to flee while he petrifies himself, preventing the Mysterious Girl from taking the Crystal.
When the Mysterious Girl threatens to shatter Palom's body to obtain the Crystal, Leonora attempts to fight her off. Palom recovers, and it is revealed Leonora was the girl Palom was flirting with during the ending of Final Fantasy IV. They band together, but are defeated by Shiva. The Mysterious Girl steals the Crystal and vanishes. Meanwhile, on Mount Ordeals, Porom has encountered Kain and senses something has happened to Palom.
Edge's Tale: The Pulse of BabilEdit
The members of The Eblan Four -- a group of Ninja under Edge's command, have witnessed and survived the attacks lead by Kain and the Mysterious Girl: Gekkou was entrenched with Yang's monks, Zangetsu was with the dwarves, Izayoi was disguised as a Troian priestess, and Tsukinowa was among the mages of Mysidia.
Edge sets out to infiltrate the Tower of Babil where the Eblan Four appear one by one to assist him. They travel to the peak where they find the Mysterious Girl. Though unable to defeat her and the summoned Ifrit, Edge refuses to submit and the team dives out of the tower, and land safely aboard the Falcon's deck. Edge reunites with Rydia and recognizes the Man in Black.
Porom's Tale: The Vanished Lunar WhaleEdit
During Palom and Porom's childhood the two attended magic lessons with the Elder of Mysidia. One day, Palom cut class and tried to impress a group of girls, including a young Leonora. When found and confronted by the Elder, Palom revealed his desire to follow in Tellah's footsteps, and the Elder agreed to let him follow his dream.
Years ago, Palom and Porom went on a trip to visit Rydia ferried by Cid and his airship because the Devil's Road was closed. Palom asked Rydia to take him into the Land of Eidolons to learn about summoning magic. They visited the dwarves and Luca tagged along. but Rydia had to turn back when she was forbidden entry to the Land of Eidolons.
Returning to the present, Porom is praying and senses her brother has arrived safely in Troia. She discusses her desires to become independent when the Elder asks why she did not accompany him, but they are interrupted when he senses a disruption. They find the mages of Mysidia gathering near the Sea of Mysidia as the Lunar Whale rises up out of a whirlpool, floating towards the second moon. Needing the skills of a Dragoon, Porom sets out for Mt. Ordeals with a Black and White Mage to track down Kain.
Atop Mount Ordeals, they find the tomb of Cecil's father, Kluya, and hear his spirit speak of his sons. They locate Kain and, after explaining the situation and having a brief disagreement, set out to Mysidia together and find it under attack by the Mysterious Girl. Kain, wishing to travel to Baron, leaves the Elder and Porom to defend the town. The two battle the Mysterious Girl (who summons Ramuh) and are defeated, with the Elder injured. Kain reappears with the Crystal, offering it to the Mysterious Girl in exchange for his service and a chance to see Cecil. The Mysterious Girl agrees and vanishes, and Kain leaps away, ignoring Porom.
Edward's Tale: Star-Crossed DamcyanEdit
Damcyan has been rebuilt. King Edward's secretary, Harley, goes off to investigate a disturbance but doesn't return. Edward and three soldiers go out to look for her and when they find her the party returns to Damcyan. Damcyan is surrounded by the Red Wings and Edward and Harley go through the cave to Kaipo, but Harley falls ill to the Desert Fever.
During the night, the spirits of Anna and Tellah visit Edward. Tellah tells Edward Anna wants him to ask what his heart wants, possibly meaning he should find a new partner. Edward fetches a sand pearl from the Antlion's Den to cure Harley without the Damcyan guards' assistance. With Harley recovered, they board a ship to Baron and talk to Cecil. Edward notices Cecil is acting strangely, and leaves some Whisperweed in his throne room to eavesdrop on him and discovers Cecil is plotting with the Mysterious Girl. They head back towards Damcyan and witness Yang and his ship being swallowed by Leviathan.
Kain's Tale: Return of the DragoonEdit
At Mount Ordeals, Kain rescues Porom and the mages from the monsters. The party returns to Mysidia, where he betrays her and takes the Crystal. He follows the Mysterious Girl back through the Devil's Road.
Meanwhile, Ceodore's party makes its way over the Mist mountain range to Damcyan. Ceodore reaches Kaipo, where Baron soldiers attack him in the middle of the night. Ceodore and the Hooded Man head through the water cave and encounter and defeat the Octo-Kraken.
The Red Wings have surrounded Damcyan and Kain retrieves the Crystal for the Mysterious Girl while also kidnapping Rosa. Edward and Cid, who arrive with the Enterprise, accompany Ceodore back to Baron. They encounter Kain and the captured Rosa in Castle Damcyan and upon confronting Kain, discern he is Kain's dark half who defeated his light half (the Hooded Man) on Mount Ordeals. The Hooded Man (Kain) regains his Jump ability, equips his lance, and defeats his dark half. Kain accepts his dark half as being a part of him and merges with it, becoming a Holy Dragoon. The group goes on to confront Cecil and the Mysterious Girl.
Lunarian's Tale: The Blue Planet That WasEdit
The Man in Black's identity is revealed to be Golbez. Some time ago, on the Red Moon, Golbez noticed Fusoya missing. He went through the Lunar Subterrane, finding Fusoya and helping him in his investigation. The two headed to the Lair of the Father where they found a petrified Bahamut. They headed to a cave where they confronted the Mysterious Girl. They battled her and she summoned Asura.
She escaped back to the Crystal Palace, where she and Leviathan fought Golbez and Fusoya. Again she escaped, and they followed her into the Lunar Subterrane where the Mysterious Girl was waiting for them. She resurrected Zeromus himself, and Golbez and Fusoya fought him. Zeromus used Big Bang, which began to destroy the palace.
Fusoya teleported Golbez out who took the Lunar Whale and headed to the Blue Planet. During the ride he dreamed of being possessed by Zeromus in the past.
Gathering's Tale: The Moon's GravityEdit
Rydia's party (with Luca, Edge, and Golbez) notice the moon turning crimson and approaching the Earth, with meteors damaging the planet. The party tries to enter Baron Castle but it is guarded by an Eidolon's force field. The party flies to Mist, and Rydia's mother's spirit advises them that the force field will be broken if they save the other Eidolons from their mind control.
In Kaipo, Yang and Ursula are found passed out. At Fabul, the party gets the frying pan and a ladle from Sheila and when they give Ursula the ladle and whack Yang with the pan, they wake up and join, along with the Sylphs. Troia is covered in ice and inside the Lodestone Cavern, Shiva is holding the place under a spell; after defeating her, Rydia either gains her as a summonable Eidolon or destroys her. Palom and Leonora join after Troia is thawed.
Eblan is engulfed in flames in Ifrit's possession. Edge tells everyone to flee so he may take Ifrit on by himself, but is defeated. Rubicante (the former head of the Archfiends) appears, and gives Edge a clue on how to defeat Ifrit. Edge bands together with Rydia to defeat Ifrit with Rubicante's Inferno skill and upon Ifrit's defeat, he rejoins Rydia.
In Mysidia, the party fights Ramuh and recruits Porom. They head to Agart and fight Titan, who opens a rift in the ground, swallowing the party. After climbing back up through Agart's well, Porom appears briefly to assist them by casting Float on everybody, rendering Titan defeatable. After Titan has joined them, the party drags an exhausted Porom back to the Falcon. They return to Mist, where the Mist Dragon joins Rydia.
The party journeys to Baron Castle where they break the force field. Ceodore's party (with Kain, Rosa, Edward, and Cid) fights the possessed Cecil and Odin who comes to his senses and knocks Cecil out of his possession. While the others nurse Cecil, Ceodore joins with Rydia, Golbez, Rosa, and Edge to take out the Mysterious Girl. She dies, but dozens of her appear and tell the party they are awaiting on the True Moon. Golbez calls the Lunar Whale to chase after the girls.
Final Tale One: True MoonEdit
The Lunar Whale is parked outside of the Subterrane of the True Moon. Cecil can barely talk or recognize the world around him. In the crater dungeon the eight Crystals are scattered about and each contains a boss fight. At the end Cecil and Golbez fight Dark Knight Cecil, who uses a special attack to bring everyone to near-fatal status. He tries to kill the party members one by one but Cecil blocks each hit. When the Dark Knight attacks Cecil, Golbez guards him, taking a mortal blow. If the party contains Golbez, Ceodore, Cecil, and Rosa when they encounter the Dark Knight, Golbez will survive. Cecil regains his lost strength and White Magic and claims the Excalibur. After the battle, Cecil thanks Golbez and the party, and heads to a warp tile.
Final Tale Two: Planet EaterEdit
The party continues on to encounter Crystals containing bosses. The party encounters the Mysterious Girl, who summons Bahamut, but if Rydia has tamed Asura and Leviathan, Bahamut will come to his senses and turns on the Mysterious Girl, pushing her back. Several clones confront the party, revealing the Mysterious Girl's name to be Maenad. They discover a child Maenad who opens the door leading to the True Moon's core. The party reaches The Creator, the last surviving member of a species which once prospered on the distant edge of the universe, but destroyed its own civilization. Wishing to conduct experiments regarding the evolution of life it created a host of Crystals capable of recording the history of a world and distributed them upon planets which held the promise of life.
The Creator mass-produced and dispatched the Maenads to recover the Crystals. It deems the Blue Planet's races evolutionary failures whose continued existence cannot be permitted, and, like the worlds of other inferior races, attempts to devour the Blue Planet with the True Moon, which is revealed to be the remains of a space fleet once manned by the Creator's race.
The party engages The Creator and after defeating it, the area begins to explode. Pausing only to rescue the child Maenad, the party retreats as The Creator pursues them and multiple Maenads appear to protect the party and the child Maenad. As he dies from a final Meteor spell cast by a Maenad, The Creator thanks the party and perishes.
The True Moon leaves the planet's orbit and the Lunar Whale returns to Earth with the party intact, along with the child Maenad. The Troia priestesses offer Leonora a position, but she declines. Izayoi, disguised as one of the women present, laughs. Leonora heads off to Mysidia where Palom and Porom are with the Elder, who offers them a joint position as the leaders of Mysidia. Palom complains about not being ready or wanting to handle the responsibility. Leonora asks Palom and Porom to train her as a sage now that she has quit the priesthood. Tsukinowa, disguised as a frog, is keeping watch.
At the Dwarven Castle, Giott and Luca are approached by Cid and Mid (Cid's grandson), who go to work on an airship, trying to figure out how to power it with the Crystals' magic (with a disguised Zangetsu watching on). They plan to disarm all weapons. In Fabul, Yang trains Ursula himself, reminding her he is not going to go easy on her just because she is his daughter. Gekkou admires the kingdom's strength. In Damcyan, Edward and Harley observe the Crystal. Although pulled away by an elder for discussion about Cecil's plan to amass the material needed to rebuild the damage caused to the Blue Planet since the moon meteors nearly destroyed it, Edward sees the spirits of Tellah and Anna, and thanks them.
Edge leaves Eblan Castle for Mist. He dismisses the Eblan Four, but they swear to await further orders. In Mist, Rydia is raising the child Maenad, now named Cuore. Leviathan and Asura arrive, saying they figured that since Rydia was unable to make it into the Feymarch last time she tried, it was their turn to pay her a visit. Edge arrives to see Rydia and Asura reveals he was the one who invited them.
In Baron Rosa referees a sparring match between Cecil and Ceodore. Kain, the new leader of the Red Wings, drafts Ceodore for a new quest: to travel the world rebuilding the damage caused by the meteor attack. Rosa and Cecil think of Golbez, who has taken the Lunar Whale to look for Fusoya and the other Lunarians. Biggs and Wedge's spirits appear behind Kain as he warns Ceodore they would be disappointed if he whines. They board the airship with Luca and Cid as they head off to Damcyan meet Edward and Cecil to gather materials.