The story of Final Fantasy IX follows the thief Zidane, a member of the Tantalus Theater Troupe that sets out to kidnap the princess of Alexandria, Garnet Til Alexandros XVII. The war between kingdoms reveals an undercurrent plot that endangers the world of Gaia and Zidane and the friends he meets along the way become entangled in the quest to save it.
Kidnapping the princess
Queen Brahne Raza Alexandros XVI of the kingdom of Alexandria lusts for power, and seeks to increase her domain by conquering the surrounding lands. Regent Cid of Lindblum worries how this will impact Princess Garnet, and dispatches the Tantalus Theater Troupe to kidnap her.
The princess yearns to escape from her wicked mother and willingly boards the Theater Ship. During the operation Vivi, a lone black mage, and Adelbert Steiner, Captain of the Royal Knights of Pluto, become involved. During their escape the Theater Ship is shot down and crashes into the Evil Forest. Brahne is outraged Garnet escaped with a valuable crystal, a royal heirloom, and dispatches the Black Waltzes to retrieve her.
One of the members of Tantalus, Zidane, wants to find the missing princess, but their leader Baku dissents and dismisses Zidane from Tantalus. Vivi and Steiner join Zidane in rescuing Garnet from the forest's carnivorous flora and escape the woods, leaving Tantalus behind. The escapade rouses the forest made sentient by the Mist and petrifies itself. Mist is a malevolent substance whose influence hardens people's hearts and makes regular animals into ferocious monsters. It covers the lower reaches of the Mist Continent and thus most kingdoms opt to build their empires on the plateaus above it.
A Tantalus member, Blank, wishes to aid Zidane, but when delivering him a map of the rarely-traversed surface of the Mist Continent, he gets caught by the forest vines and petrified along with the woods. Zidane, Garnet, Vivi and Steiner pass through the Ice Cavern to get above the Mist, and Zidane defeats Black Waltz 1, Brahne's lackey sent to retrieve Garnet's royal pendant. Before arriving in the village of Dali, Garnet adopts the alias of "Dagger" to blend in with the peasantry. The villagers kidnap Vivi and the party is shocked when they rescue him and discover the villagers are manufacturing black mages, automaton dolls who cast powerful magic, from the Mist for export to Alexandria.
Garnet ponders returning to Alexandria to confront her mother about the black mage business, a notion Steiner approves of. After besting Black Waltz 2 they board a cargo ship piloted by automaton black mages. They come under fire from Black Waltz 3 and Vivi, Zidane, and Steiner confront the golem leaving the journey's destination in Garnet's hands. The princess hesitates, but ultimately decides to head for Lindblum, resulting in an erratic flight through the South Gate crashing the Black Waltz's airship.
The four meet with Regent Cid in Lindblum. They are surprised to find he has been turned into an oglop, an insect most find disgusting, by a magic spell from his absconded wife, Hildagarde Fabool. Cid refuses to mobilize against Alexandria for fear of leaving his borders unprotected. While Lindblum hosts the Festival of the Hunt Brahne's black mage army advances into Burmecia, home of Zidane's friend Freya Crescent who aids him during the festival. Zidane wants to accompany Freya to Burmecia and Vivi wishes to come along to learn more about the black mages; he has no memory of his past beyond being cared for by his late "grandpa" Quan, and fears he may not be human.
Cid orders Garnet to remain in Lindblum. In retaliation, she tampers the festival feast with sleeping weed and absconds with Steiner back to South Gate. The others venture to Burmecia, recruiting the gluttonous Quina Quen along the way. They find Burmecia abandoned and decimated by Brahne's black mage army. At the city apex they meet the queen along with General Beatrix and a mysterious man named Kuja. Beatrix defeats Zidane's group, and Brahne sets her sights on the isolated kingdom of Cleyra.
Meanwhile, Garnet and Steiner run into Marcus from Tantalus, who wants to save his friend Blank from the Evil Forest, but needs an item known as Supersoft to heal his petrification. Garnet feels culpable for Blank's fate and agrees to help in Marcus's quest much to Steiner's dismay. The three are attacked by the malfunctioning Black Waltz 3 and destroy him for good, before making their way to the city of Treno where they sneak into the basement of a noble's mansion. The noble turns out to be Garnet's old tutor, Doctor Tot, who relinquishes the Supersoft willingly and advises the three to take the Gargan Roo pathway to Alexandria where Garnet meets with her mother and Marcus and Steiner are imprisoned.
Zidane, Freya, Vivi and Quina head for Cleyra where the Burmecians are said to have evacuated. They make their way into the city perched atop a colossal tree hidden behind a perpetual sandstorm. They warn the Cleyrans of the impending attack, and the Cleyrans perform a ritual to strengthen the sandstorm that protects the village. Something goes wrong and the sandstorm dissipates. Brahne has turned on the princess and ordered Garnet's eidolons extracted—magical creatures of legend. The queen's court jesters, Zorn and Thorn, extracted Garnet's eidolons into summoning gems and Brahne uses the eidolon Odin to obliterate Cleyra after Beatrix steals the nation's jewel. Zidane's crew hitches a ride on the Alexandrian airship Red Rose back to Alexandria Castle, leaving Quina behind.
Steiner and Marcus have broken free from imprisonment with Marcus departing for the Evil Forest to save Blank. Zidane's party joins forces with Steiner and they free Garnet from Brahne's clutches with the assistance of the enlightened Beatrix. While Steiner, Beatrix and Freya stay behind to secure their escape, Zidane, Vivi, and Garnet attempt to use the gargant system to flee back to Treno. Their ride is spooked by a monster and they crash in Pinnacle Rocks where they meet the eidolon Ramuh. Having again lost Garnet, who still holds the royal pendant, Brahne hires two bounty hunters—Lani and Amarant—to capture her and kill Vivi, whom Brahne considers a rogue black mage.
Garnet is ambivalent on the power of eidolons that had remained latent within her without her knowledge, and that have now been stolen to be used by Brahne. After passing Ramuh's trial, giving Garnet the power to summon him, the three witness the invasion of Lindblum by a black mage army and another eidolon, Atomos. Sneaking into the surrendered city, Zidane and Garnet meet with the now powerless Regent Cid who reveals Kuja is the one supplying Brahne with the black mages. It is rumored the origin of Mist, the main ingredient in black mage production, lies in the Outer Continent, and the party sets off to locate Kuja there.
They run into Quina at Qu's Marsh who had escaped Cleyra and returned to their home. Quina helps the party locate the entrance to Fossil Roo, an ancient route said to lead to the Outer Continent. The party is accosted by Lani on her quest to retrieve the princess, but they defeat her. On the Outer Continent the party finds the Black Mage Village where many sentient black mages like Vivi live, having defected from the Alexandrian army and founded a settlement far away from conflict. Vivi discovers black mages have a lifespan of about one year, and many of the earliest builds of black mages have already started to "stop".
After passing through the dwarves' village of Conde Petie they meet Eiko Carol, a young girl and last of the summoner tribe, who leads the party to her home of Madain Sari. They find Madain Sari is a ruined village where Eiko lives alone with a group of moogles, and Garnet learns the truth of her past: she is a summoner born in Madain Sari, but in the aftermath of the village's destruction ten years ago, she had washed up in Alexandria where she had replaced the recently deceased Princess Garnet. Having lost her memories in the calamity, Garnet was raised believing Queen Brahne was her mother, never having learned she possessed eidolons.
Zidane convinces Eiko to open the path to the Iifa Tree, a giant tree that towers over the landscape and is mysteriously shrouded in Mist despite the rest of the continent being free of it. The group descends down the trunk all the way to the core of Gaia where they encounter Soulcage who reveals the Mist's true purpose: Mist is the by-product of the Iifa Tree's true function, stopping Gaian souls from returning to their crystal in the planet core while letting the Terran souls cycle freely. Mist arises from the refining process and is directed onto the Mist Continent via the Iifa Tree's roots that cover the whole planet within its crust. The malevolent substance is responsible for the monsters that roam the depths of the continent, and incited war among the nations until Mist-powered airships were invented.
Upon Soulcage's defeat the Mist dissipates, and the heroes return to Madain Sari where they find the bounty hunter Lani and her brooding companion Amarant. Upon finding an identical crystal in Madain Sari to that of Garnet's royal pendant, Lani takes Eiko hostage. Amarant no longer tolerates her methods and turns against her, driving her away, and joins Zidane's party.
They leave Quina in Madain Sari and return to the Iifa Tree and find Kuja. Queen Brahne and her navy appear off Iifa's coast to challenge him, as Brahne no longer considers him useful, having attained the power of eidolons. Kuja summons his Silver Dragon and monsters of Mist to repel her, and Brahne retaliates by summoning Bahamut. Kuja calls the airship Invincible to enslave it. Now under Kuja's command, Bahamut wipes out Brahne and her soldiers and black mages with a devastating Mega Flare.
A dying Brahne washes up on the shore and with her final words apologizes to Garnet who must now become the queen of Alexandria. Alexandrian forces retreat from Lindblum and Garnet inherits the jewels her mother had stolen from the kingdoms she had conquered. Garnet shares the jewels with Eiko—each keeping two—to reinforce their bond as the last of the summoner tribe. Zidane is distraught he must part with Garnet for whom he had begun to have feelings for, and departs to Treno with the others to participate in a Tetra Master tournament.
The ceremonies of Garnet's coronation are short-lived as Kuja summons Bahamut to destroy Alexandria. The others fly in from Treno with Regent Cid's experimental airship, the Hilda Garde II, that can operate without Mist. Eiko and Garnet bring together the fragments of the ancient divided summoning gem, the true reason Brahne kept pursuing Garnet's royal pendant, and summon Alexander, the holy eidolon guardian of Alexandria, that vanquishes Bahamut. Kuja, in awe of its power, calls for the airship Invincible to enslave it. A mysterious elderly man appears aboard the Invincible, reproaches Kuja for his rebellion, and destroys Alexander and a majority of the city. Kuja, left without an eidolon, flees.
Garnet is rendered mute by the trauma of seeing her kingdom decimated, and she, Zidane and their friends, now including Steiner and Freya, take refuge in Lindblum. Cid's mind is not what it used to be as an oglop, and thus his newest airship, the Hilda Garde II, is poorly designed. The party sets to find a cure for Cid but turns him into a frog instead. The party is reunited with Quina who has washed ashore in Lindblum, and Cid gives the party the ship Blue Narciss to track down Kuja, accompanying them on their quest.
They stop by the Black Mage Village and discover Kuja has tricked the black mages into following him by claiming he knows how to extend their lifespan. Now knowing where Kuja resides, the group infiltrates his Desert Palace but falls into a trap and becomes imprisoned. Kuja forces Zidane and three of his friends to fly to the Forgotten Continent and retrieve the Gulug Stone from Oeilvert in exchange for the life of their other friends. It turns out Kuja possesses Hilda Garde I, Cid's new airship model that can fly without Mist that Hilda took when she left him after having turned him into an oglop.
Oeilvert turns out to be an ancient archive from a lost Terran civilization with many artifacts, including an ancient eidolon, Ark, which must be defeated to obtain the Gulug Stone. To Zidane's surprise, only he can decipher the language of Terra though he has never heard of this other world.
Meanwhile, Regent Cid and the remaining party members break free and shut down the palace security system, Valia Pira. Kuja snatches the Gulug Stone from Zidane and absconds with an abducted Eiko to Mount Gulug where Kuja wishes to obtain an eidolon stronger than Alexander. He believes this would let him defeat Garland, the old man who had appeared aboard the Invincible. The heroes pass through Esto Gaza to track him down, and witness Zorn and Thorn—Brahne's jesters who now obey Kuja—attempt to extract Eiko's eidolons although she is too young to withstand the ritual. Mog, Eiko's pet moogle, reveals her true eidolon form through Trance, a surge of powerful emotions that momentarily enhances one's inner capabilities. With her help the court jesters are destroyed.
Having witnessed the power of Trance Kuja deduces he doesn't need a new eidolon after all. Unable to naturally enter Trance, Kuja formulates a plan to assimilate enough souls to enter a form of permanent Trance; as Kuja is a Genome originally constructed as a vessel for Terran souls, he can absorb them and wishes for all the gathered souls to simultaneously enter Trance to become all-powerful. While Kuja flees Zidane's party finds Queen Hilda, Cid's estranged wife who fled Lindblum after an argument with her husband, and escorts her back to Lindblum.
Hilda makes amends with Cid and turns him back into human. Cid puts the finishing touches on his new airship, the Hilda Garde III. The black mages have realized Kuja was using them and return to the Black Mage Village. Garnet returns to Alexandria to visit her mother's resting place. When Zidane follows her she recovers from her silence, takes his dagger and cuts off her ponytail in a promise to continue to fight for her people and her adoptive mother.
Queen Hilda had been abducted by Kuja after she went missing as he had needed her airship, the first Hilda Garde. While captive, she learned of his plans and tells the party of Kuja's ambitions and that he hails from the planet of Terra. She directs them towards Ipsen's Castle on the Forgotten Continent. Within the inverted structure the party finds four elemental mirrors: seals to the portal to Terra. After defeating the worm-like Taharka and rescuing Amarant from his own arrogance, Zidane forms four parties to secure each elemental shrine simultaneously. The defeat of the four guardians, and placing the mirrors to the shrines opens the path to Terra through the Shimmering Island.
Terra is a mysterious dead planet that exists on the inside of Gaia. Millennia ago Terra had an advanced magical civilization and its inhabitants wished to become immortal and preserve their culture for all time. The life source of all planets in the cosmos is a crystal at the planet core that collects the memories of all living beings when the souls of the dead return to it at their life's end. Terrans' wish for immortality disrupted the natural order, and when the Terran crystal weakened the Terrans assimilated other planets' crystals to preserve themselves.
Thousands of years ago Terra attempted to fuse with Gaia, but it ended with disaster and Terra shifted to the inside of the planet of Gaia. Terra's red moon moved to Gaia's orbit, and many Terran landmarks appeared on Gaia, such as Terra's magical tree of Iifa, and Oeilvert. Terrans tasked the android Garland, the old man who annihilated Alexandria and whom Kuja wishes to vanquish to become the overlord of Terra and Gaia both, with restoring Terra to its former glory before entering a deep rest. Garland crafted the Genomes to be used as vessels for the Terran souls when the time would be right for Terra to assimilate Gaia whose crystal has been deprived of its natural soul cycle by the Iifa Tree for thousands of years. Kuja was one of Garland's creations whom he sent to Gaia to incite war to amplify the rate the souls would attempt to return to the crystal. Kuja's will was strong and he rebelled against his creator, knowing that if Garland's plans were to succeed he would no longer need Kuja and make him into a regular Genome.
In Terra the party meets the Genome girl Mikoto who leads the party to the Genome village of Bran Bal. Garnet glimpses the Invincible stationed outside the village and reclaims the memories of the time the airship destroyed Madain Sari and passes out. While the others care for her, Mikoto tells Zidane he is a Genome from Terra made by Garland to one day succeed Kuja, as after Kuja was created Garland had seen the errors in his design of having created him as an adult, rather than as a child capable of emotional growth. She leads Zidane to Garland who confirms everything and, horrified by what he has learned, Zidane attempts to fight him. Garland reluctantly decides to discard Zidane and make him a regular Genome and seals him within the Pandemonium, a palace where the ancient Terran souls rest. Garland fails to remove Zidane's soul and Zidane's friends free him and they confront Garland together.
Kuja has followed the party into Terra on his Silver Dragon and stolen the Invincible. He showcases his new mastery of Trance, achieved by draining the souls held within the airship and using the soul of a hateful person—Queen Brahne—as catalyst. Kuja dispatches the party with an Ultima spell and announces he will rule both Terra and Gaia. Garland warns him that his power is meaningless, but Kuja kicks his old master off Pandemonium's precipice to his death.
Garland remains as an omniscient voice and from beyond the grave tells Kuja his new-found goal is for naught; a limit on his lifespan was set when he was created, and his demise is fast approaching. Kuja's euphoria turns into rage and in his vanity he deduces that if he is going to die, he will take the world with him. Kuja obliterates Terra with wave after wave of Ultima spells, and the party and resident Genomes escape aboard the Invincible back through the Shimmering Island to Gaia. Mist has returned to the world, now enveloping the entire planet, flowing once more from the Iifa Tree.
While the Genomes move in with the black mages in their village, the party finds the foreboding entrance to Memoria hovering above the Iifa Tree, where Gaia's memories and Kuja await. The armies of Alexandria and Lindblum stave off the horde of Silver Dragons blocking Memoria's entryway and Invincible breaks through, carrying the party into Memoria that leads them back in time. Memoria is a place made manifest from the memories stored within Gaia's crystal, and the party witnesses the significant moments of their lives intertwined with the earliest stirrings of Gaia. Garland's lingering voice guides them through the dimension before leaving them at the entrance to the Crystal World, a realm where time does not exist, only memories of every life originating from the first crystal where all planets are born from.
Saving reality / epilogue
After traveling through Memoria to the beginning of all time to the Crystal that is the lifesource of the universe, they find Kuja, intent on destroying it. Zidane and his friends face Kuja in battle, and in a last effort Kuja devastates the party with Ultima. The party awakes on the Hill of Despair, finding themselves in the presence of Necron. It is a deity-like being roused by Kuja's nihilism that arises to deny all existence by returning the world to the Zero World, a world without a Crystal, as he sees the suffering of living beings arising from their fear of death. The party defeats Necron who marvels at the party's will to persist even knowing they cannot escape death, and heeding their desire, departs.
Kuja uses the last of his strength to teleport the heroes onto the banks of the Iifa Tree. The others return to Alexandria on Cid's Hilda Garde III while Zidane searches for Kuja. He locates Kuja deep within the dying Iifa Tree, and as the latter accounts for his sins the collapsing tree's roots converge on them both.
Some time later Tantalus returns to Alexandria to perform I Want to Be Your Canary for Queen Garnet. Vivi has died, having come to the end of his lifespan, but as a legacy copies of him have been made, now known as "Vivi's sons." Though Vivi was unable to say goodbye to Zidane, he reminiscences on his time with the party in a soliloquy, thanking Zidane for helping him come to terms with his existence.
Everyone gathers up in Alexandria to see the play, Freya having found her lost love, Sir Fratley, and the two are repairing their relationship despite Fratley's amnesia. Amarant arrives with Lani, Quina works as a chef in the Alexandria Castle, and Eiko has been adopted by Cid and Hilda. Beatrix and Steiner, now a couple, act as Garnet's bodyguards and accompany her on the balcony where she watches the play. During the play a shrouded form masquerading as Marcus casts off his cloak to reveal a returning Zidane. Alexandria celebrates, old friends cheer from the stands, and the queen runs through the crowd and leaps into Zidane's arms.