The story of Final Fantasy IX follows the exploits of a young genome named Zidane Tribal and his companions as they attempt
to prevent a world war on the planet Gaia. The scope of the game expands when it is revealed that the recent warfare is merely
a part of a greater plot for the planet Terra to assimilate Gaia into itself. A large portion of the story takes place before
the events of the game and are revealed through flashbacks and dialogue.
Five thousand years before the events of the game, the unnamed race of people from the planet Terra realized that their
planet was dying. To save themselves they devised a plan to assimilate Gaia, a method of survival that they had performed
many times in the past. To this end, they created Garland to be the caretaker of their world and the soulless Genomes to be
vessels for their souls to inhabit once the assimilation was complete. Then the people of Terra went to sleep in a form of
Suspended animation, the exact mechanics of which are unknown. Notably, it is always their souls that are referred to as sleeping,
what has occured to their bodies is not revealed. Garland then created the Iifa Tree to work as a siphon for souls. Its role
is to halt the flow of souls on Gaia, thus emptying Gaia of it's souls once all life has ceased. To speed up this process,
Garland created a genome with a soul, Kuja, to be an "Angel of Death" and incite warfare among Gaia.
However, Kuja proved to be too ambitious for Garland's liking, so Garland created Zidane, a more powerfull "Angel
of Death," to eventually replace Kuja. Jealous of Zidane's greater power, Kuja abducted Zidane and abandoned him in Lindblum
on Gaia when Zidane was still very young. Zidane was adopted by Baku, the leader of Tantalus (acting troupe and thieves' band),
who raised him as his own son and to be a member of Tantalus. After losing Zidane, Garland created a third even more powerful
"Angel of Death" named Mikoto, but later decided not to use her. Kuja continued to serve Garland as "Angel
of Death" on Gaia, all the while searching for a power great enought to allow him to usurp Garland. Fearing the power
of Eidolons, Garland used the ship Invincible to destroy Madain Sari, the village of Summoners. Eiko Carol, a Summoner, was
out of town with her family that day and survived, though her parents died later. Another Survivor of the village's destruction
was a woman who escaped with her young daughter by boat. Though the woman did not survive, her daughter was recovered in Alexandria
and was adopted by Queen Brahne and the King to replace their own late daughter, Princess Garnet. Meanwhile, Kuja began producing
the Black Mages out of Mist (the stagnant souls released by the Iifa Tree) to serve as an army for him to sell as an arms
dealer, in the hopes of inciting global warfare.
Kuja's appearance in Alexandria Castle coincided with a change in behavior for Queen Brahne in the form of raised hostilities
towards other kingdoms. Worried about his niece, Princess Garnet, Regent Cid arranges for Tantalus to perform a play in Alexandria
as a cover for kidnapping Princess Garnet and bringing her back to Lindblum where he could keep her safe. After hearing of
this upcoming performace, Princess Garnet planned to run away and sneak aboard the Prima Vista, the Tantalus Theatre ship,
and ride it back to Lindblum where she could speak with her Uncle, Regent Cid, about her mother's erratic behavior. The game
begins at this point with Zidane and the rest of Tantalus coming to kidnap Princess Garnet. The kidnapping/running-away plot
is discovered by Queen Brahne who then attacks the Prima Vista, crippling the ship and causing it to crash-land in Evil Forest.
Steiner, captain of the Knights of Pluto, and Vivi Orunitia, the abandoned prototype for the Black Mage dolls, are both caught
up in the hectic escape and must now travel with Zidane and Princess Garnet. Captain Steiner continues traveling with the
party to serve as Garnet's bodyguard and with the hopes of eventually escorting her back to Alexandria. Vivi continues to
follow Zidane out of mutual friendship. From Evil Forest, Zidane and company must travel cross-country to reach Lindblum while
being chased by the Black Waltzes, elite variants of Black Mages that have free will and have been dispatched by Queen Brahne
to retrieve Princess Garnet.
After Arriving safely in Lindblum, word arrives from the neighboring kingdom of Burmecia that the Alexandrian Army led
by General Beatrix have invaded Burmecia with the aid of the Black Mage Army. Regent Cid insisted that Princess Garnet remain
safely in Lindblum, so she and Captain Steiner snuck away to travel back to Alexandria so that she could confront her mother
directly. Upon arriving, Queen Brahne imprisons them and forcefully extracts Garnet's Eidolons for her own use. Having no
further need of Princess Garnet, Brahne schedules her to be executed. Meanwhile, Zidane and Vivi travel to Burmecia to help
Zidane's long-time friend, Freya, defend the city against Alexandria. After arriving too late to save Burmecia, they follow
the Burmecian refugees to Clerya, sister city to Burmecia. Shortly after they arrive the Black Mage army led by General Beatrix
arrives and invades. Clerya is ultimately destroyed by Queen Brahne using the Eidolons stolen from Princess Garnet. As a last
resort, Zidane's party follows a withdrawing black mage and learn of Princess Garnet's death setence. They use the Red Rose's
teleporter to return to Alexandria Castle, with only thirty minutes to spare before Garnet's execution. After rescuing Steiner
and Garnet, Zidane and company are confronted by General Beatrix with the result of Beatrix being convinced of Queen Brahne's
evil intentions. Captain Steiner, General Beatrix and Freya remain behind to hold off the Alexandrian Army long enough for
Zidane, Vivi and Princess Garnet to escape. Zidane and company arrive in Lindblum just in time to see Queen Brahne using Eidolons
to devestate Lindblum, forcing Regent Cid's surrender of the kingdom to Alexandrian occupation. At this point, Queen Brahne
had successfully conquered the entire Mist Continent.
Regent Cid had tracked down Kuja as the man behind Queen Brahne's recent behavior, and has traced him to the Outer Continent.
Guided to a passage leading to the Outer Continent by Quina Quen, a gourmand of the Qu Tribe, with the provision that they
take Quina with them, Zidane and company travel to the Outer Continent to track down Kuja. Along the way, they meet Eiko Carol,
the only other living survivor of Madain Sari who joins the party out of loneliness, and Amarant Coral, a bounty hunter hired
by Queen Brahne to retrieve Princess Garnet's pendent who joins the party to better understand how Zidane could have bested
him in combat. The party tracks Kuja down to the Iifa Tree. Inside the Iifa Tree, the party encounters Soulcage, an undead
being at the center who is linked to the Iifa Tree, and the source of the Mist production. The party confronted and defeated
Soulcage, stopping the Mist from being produced on Mist Continent. Upon exiting the Iifa Tree, the party witnesses as Queen
Brahne attacks Kuja at the Iifa tree with the Alexandrian Army. After she summons an Eidolon, Kuja uses the Invincible to
take control of the Eidolon and uses it to decimate the Alexandrian fleet, killing Queen Brahne.
The party returns to Alexandria where Princess Garnet is coronated. That same night, Kuja attacks Alexandria with his
Eidolon stolen from Brahne, successfully drawing out the legendary Eidolon Alexander whom destroys Kuja's Eidolon. But when
attempting to take control of Alexander with the Invincible, he is interrupted by Garland whom seized back the Invincible
and used it to instead destroy Alexander and a good portion of Alexandria along with it. Having lost the Eidolons taken from
Garnet and now the legendary Eidolon Alexander, Kuja's only hope to obtain a powerful Eidolon lay in Eiko, the only other
surviving summoner. Feeling useless to the reconstruction of Alexandria, Queen Garnet accompanies Zidane and the party in
tracking Kuja to his Desert Palace on the Outer Continent. Kuja traps the party, and using half of them as hostages forces
Zidane and the remaining party memebers to retrieve the Gulug Stone from Oielvert. Kuja attempts to betray them only to manage
escaping with the Gulug stone and Eiko as a prisoner. Zidane and company chase Kuja to Mt. Gulug where Kuja attempts to extract
the Eidolons from Eiko in the same manner that Brahne used on Garnet. The extraction is interrupted when Eiko's guardian moogle,
Mog, uses trance to transform herself into her true form, the Eidolon Madeen. Having failed his last remaining chance to procure
an Eidolon and bearing witness to the power of trance, Kuja escapes and turns his efforts instead to unlocking the power of
trance to usurp Garland.
Following Kuja to Terra, the party arrives near Bran Bal where the majority of Terra's plot to assimilate Gaia is revealed.
Zidane and company confront Garland in Castle Pandemonium. During the confrontation, Kuja snuck into the Invincible and tapped
it's reservoir of souls that it had collected to strengthen his transformation into Trance. Notably, one of the strongest
souls to fuel his transformation was that of the late Queen Brahne. After Garland was defeated, Kuja arrived to challenge
the weakened party and was promptly defeated. This defeat was enough emotional stimulation to trigger his Trance transformation.
In his new form he killed Garland. As Garland died, he revealed to Kuja that his life expectancy was at an end and that he
would soon die. Determined to not allow the world to exist without him, Kuja used his Trance abilities to destroy Terra. Zidane
and Company managed to escape with Genome refugees by stealing the Invincible. Upon returning to Gaia, it is revealed that
the Mist had returned, but this time spanned the entire surface of Gaia. Suspecting Kuja and the Iifa Tree, Zidane and company
drop off the Genomes to live in Black Mage Village, and then inspect the Iifa Tree. From a portal to Memoria emerges an army
of Silver Dragons, which are held off by the Armada of Airships from Lindblum aided by General Beatrix in the Red Rose. Zidane
and company enter Memoria and confront Kuja in Trance. After his defeat, Kuja uses his Trance abilities to destroy the Original
Crystal, the source of all life. Upon its destruction, Necron, an eternal being, appears and resolves to destroy all of creation.
After he is defeated, Memoria and the Iifa Tree collapse. The majority of the party fled from the collapse, but Zidane remained
to attempt to save Kuja and did not escape.
Some time later (enough time for Queen Garnet's hair to grow longer), Tantalus arrives in Alexandria to perform a play
for Queen Garnet. During the performance, one of the robed figures cast off his robe and revealed himself to be Zidane. The
credits roll as Garnet and Zidane embrace, while other scenes reveal that Vivi now has children, Steiner and Beatrix have
returned to their old posts as royal bodyguards, Amarant and onetime partner Lani may be courting each other, Eiko has been
adopted by Regent Cid and his wife, Freya may be causing some of her former lover Sir Fratley's amnesia to fade, and Quina,
of course, still loves food.