Final Fantasy IX story
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Disc one
Kidnapping
Final Fantasy IX begins with a nightmare sequence, one in which princess Garnet Til Alexandros XVII dreams of herself on a small boat, braving a storm. Meanwhile, the theater airship Prima Vista is flying to the kingdom of Alexandria to perform the traditional play, 'I Want to be Your Canary'. In reality, the theater crew, Tantalus, is launching a mission to kidnap Garnet. Zidane Tribal, the main protagonist, is a member of Tantalus. This section of the game also introduces the playable characters Vivi Ornitier, a young Black Mage orphan, and Adelbert Steiner, the head of the Pluto Knights from Alexandria Castle.
The Princess is successfully apprehended by Zidane, thanks to the distraction created by the Tantalus play. Ironically, the kidnapping does not bother her, for she wanted to escape Alexandria. Vivi and Steiner are soon entangled with the group. Enraged over the escape, Queen Brahne fires on the retreating Prima Vista without regard for her daughter's safety. Brahne is apparently worried that her daughter may have gone off with a pendant of some value. They escape without any fatalities, but the damage results in the ship's crashing in the nearby Evil Forest. The crash strands Tantalus, reduces the Prima Vista to wreckage, and disperses the characters throughout the nearby woods. After some disputes and close calls, the party reunites and defeats the plant "king" of the forest, causing the forest to petrify. While escaping from this spreading petrification, Blank - a member of Tantalus - is petrified, although not before throwing a map of the Mist Continent to Zidane.
From there, the party travels through the Ice Cavern in the hopes of reaching the kingdom of Lindblum. In the cavern, Zidane fights a Black Waltz - a winged black mage that somewhat resembles Vivi. Once they exit the cavern, they travel to the bucolic village of Dali. In order to disguise herself, Garnet adopts the pseudonym "Dagger," and takes to imitating the lifestyle of the locals. In Dali, they defeat the second Black Waltz and discover an underground factory that is producing black mages like Vivi. Later, they hijack a cargo ship piloted by black mages, and fly it through the South Gate to Lindblum, defeating the last Black Waltz on the deck of the airship on the way.
Lindblum and Burmecia
In Lindblum, the largest city in the world, the party discovers it was Regent Cid, the city's ruler, who ordered Tantalus to kidnap Garnet. Garnet was surprised that Cid was already concerned about Queen Brahne's unusual and suspicious behavior. Also, it is learned that Cid's best airship has been stolen by his wife, who caught him cheating and used her magic to turn him into an oglop insect. In Lindblum, the party also participates in the annual Festival of the Hunt, where they meet Zidane's friend Freya Crescent who has been attracted to the competition. After the Festival, the party regroups in Cid's castle. Zidane hears Garnet sing a beautiful melody (the game's main musical theme, "Melodies of Life,") and visits her on a balcony. Some romantic tensions arise, and when she mentions she's had trouble sleeping and requests some sleeping weed, Zidane gives it to her.
When an Alexandrian attack in Freya's home country of Burmecia is revealed, Garnet wishes to go along with the others to help. However, the Regent disagrees. During the traditional feast following the Festival of the Hunt, Dagger intoxicates the party and the Regent with the sleeping weed and takes off with Steiner. Dagger and Steiner initiate their return to Alexandria, where they will try talking to the Queen. Upon awakening, Zidane, Vivi, and Freya travel to Burmecia. At this point, it is possible to recruit a genderless creature, Quina Quen. Eventually, the party reaches Burmecia by navigating Gizamulke's Grotto. Once at Burmecia, they discover with certainty that Brahne was behind the attacks, assisted by General Beatrix and a mysterious Silver Dragon-riding man named Kuja. The party is defeated by Beatrix, who escapes with Kuja.
Disc two
Return to Alexandria
Meanwhile, Steiner and Dagger meet up with Marcus from Tantalus on their trip back to Alexandria. They travel through the city of Treno, where Marcus finds a special item that he can use to remove Blank's petrification. While locating it, they meet Dagger's former tutor, Doctor Tot. He shows them a secret passage to Alexandria Castle called Gargan Roo. When they arrive at the castle, they are ambushed by Zorn and Thorn, Brahne's jester-like henchmen. Steiner and Marcus are imprisoned while Zorn and Thorn begin to extract Dagger's Eidolons - her magical summon spells - for Brahne's use.
The survivors from Burmecia, along with Zidane and the party, retreat to the ancient tree-top sanctuary of Cleyra. While they are resting there, Cleyra is attacked by Alexandria. This time, Brahne uses an Eidolon, Odin, to all but destroy the tree on which the city was built. Before it's destroyed, the party stowes aboard Brahne's Alexandria-bound airship, the Red Rose.
In Alexandria castle, Steiner and Marcus escape their imprisonment only to meet up with Zidane and crew. Marcus leaves to save Blank in the Evil Forest, while the rest of the party stays to rescue Dagger from Zorn and Thorn. They then convince Beatrix to join their side. Steiner, Freya, and Beatrix stay behind to help fight off the monsters that are sent after the party while Zidane, Vivi, and Dagger try to escape the way they came in, through the Gargan Roo. This time, they overshoot Treno thanks to a monster attack and end up at Pinnacle Rocks, outside of Lindblum.
At Pinnacle Rocks, they meet Ramuh, the thunder god and an eidolon, who convinces Dagger that she needs to learn to use her powers. When the group leaves Pinnacle Rocks, they see Alexandria attacking Lindblum. Brahne uses another eidolon called Atomos who ravages the city. When the party enters Lindblum, they find the city in ruins and meet with Regent Cid. They form a plan to go to the Outer Continent to find and defeat Kuja, since his influence led to Brahne's unusual behavior.
A distant land
In order to reach the outer continent, the party must travel through Qu's Marsh and Fossil Roo. At Qu's Marsh, Quina joins the party for (possibly) the second time. Along the way, they fight a bounty hunter, Lani, that Queen Brahne hired to take back the royal jewel that Dagger possesses.
In the outer continent, they reach a town called Conde Petie, the home of a group of dwarves. There, the party learns about a hidden village occupied entirely by black mages. As they travel, they learn and discover that some of the black mages had developed sentience, like Vivi had. Some of the black mages have "stopped moving" - and it makes Vivi concerned about how long he has before he stops. The party also discovers that Kuja is in the northwest corner of the Outer Continent, so the party goes back to Conde Petie and travels along the Mountain Path. There, they meet a young girl named Eiko Carol, who lives with several Moogles in the ruins of the summoner village called Madain Sari. They party goes from there to the Iifa Tree, where they find out that the mist that was constantly present in the main continent was being produced there. They defeat the Soulcage, which was responsible for creating the mist, and then escape back to Madain Sari.
At Madain Sari, the bounty hunter that attacked them earlier tracks them down and holds Eiko captive. However, she is chased off by the other hunter that Brahne hired, Amarant Coral, who then is defeated by Zidane. After he's beaten, Zidane convinces Amarant to join the party. Dagger also realizes that she was originally from Madain Sari, but was somehow transported to Alexandria when she was six. The party returns to the Iifa tree and finds Kuja, but before the fight can ensue Alexandria attacks the Iifa tree. Queen Brahne summons another Eidolon, Bahamut, to attack Kuja. However, a strange eye appears in the sky that turns Bahamut against Brahne - his fireballs destroy her battleships. The party finds Brahne lying on a beach where she says a few last words to Dagger, and then dies.
Disc three
Kuja's wrath
Back at Alexandria, Princess Garnet is being prepared for her coronation, following the death of her mother. Doctor Tot gives Dagger the stones that contain the eidolons Zorn and Thorn had extracted from her. The party leaves Alexandria with Doctor Tot to attend a card tournament in Treno. After the tournament, Eiko says that she heard from one of her Moogles that Alexandria was under attack.
The party flies to Alexandria in Cid's new airship, where Dagger, Steiner, and Beatrix are mounting a counteroffensive against Kuja's mosters. Kuja has summoned Bahamut to attack the city. When the party's airship is directly over the castle, a mystical light Eiko calls the "light of destiny" surrounds Dagger and Eiko. Eiko jumps from the bow and floats down to a high platform where Dagger was waiting. Their combined summoner abilities, along with the four special jewels they possess together summon the Eidolon Alexander, who protects Alexandria with his wings. Kuja attempts to control Alexander the same way he controlled Bahamut, but his efforts are thwarted by a mysterious man named Garland.
When the rest of the party gets to Alexandria, they climb the castle to find Dagger and rescue her just as Garland uses the Invincible - the airship that uses the strange eye in the sky - to destroy Alexander and damage the city. The party escapes with Regent Cid, back to Lindblum. The near-destruction of Dagger's kingdom results in the loss of her voice. At Alexandria, Cid realizes that his stolen airship was being used by Kuja, and manned by black mages. The party tries to change him back from an Oglop via a potion, but he turns into a frog instead.
Since Cid still can't finish his new airship with an amphibian's brain, the party takes a boat, the Blue Narciss, to the Outer Continent. After some investigation, they find Kuja's Desert Palace. Upon arriving at the Palace, the party is taken captive by Kuja. Zidane awakes in a cell with Regent Cid. Holding the life of Zidane and his companions in his hands, Kuja offers to spare their lives if Zidane retreives the Gulug Stone from Oeilvert on the Forgotten Continent. A magic barrier prevents Kuja from retrieving the stone himself. Kuja sends Zidane, along with three companions and Zorn & Thorn, to the north of the Forgotten Continent on the Hilde Garde I.
Zidane and his party head south to the Oeilvert, where they observe a series of holograms about the history of airships and the history of a place called Terra. The holograms have text in a language only Zidane can read. The party defeats the Ark eidolon and finds the Gulug Stone. Meanwhile, Regent Cid, who is still a frog, escapes Kuja's holding cell and rescues the other four party members. The party is close to escaping when Zidane returns on the Hilde Garde I. Zidane is teleported into Kuja's room, where he delivers the stone. The remaining party enters the room, but Eiko is locked out. Kuja escapes holding Eiko hostage aboard the Hilda Garde.
The party chases Kuja to Mount Gulug on the Lost Continent. At the bottom of the mountain they find Eiko facing Zorn and Thorn. Eiko's best friend, Mog, permanantly trances into the Madeen eidolon and defeats Zorn and Thorn. After a failed attempt to merge Zorn and Thorn into a powerful monster, Kuja escapes. In a room at the bottom of Mount Gulug, they find Lady Hilda Garde, Regent Cid's missing wife. The party subsequentially takes her back to Lindblum.
Terra
The following day in Lindblum, Lady Hilda turns Regent Cid back into a human. Lady Hilda holds a meeting about the information she gathered from Kuja. Hilda explains that Kuja is apparently from a planet called Terra, and the gate to this Terra is through the "Shimmering Island". But first, the party has to activate four elemental shrines. To activate the shines, four mirrors are needed from Ipsen's Castle on the Forgotten Continent. After the briefing, it is announced that Dagger returned to Alexandria. Zidane locates Dagger at Brahne's grave, where she regains her ability to speak. She cuts her hair, and they head back to Lindblum. In Lindblum, Cid has successfully completed the Hilda Garde III airship.
With their new airship, the party goes to Ipsen's Castle. Inside, they find the mirrors and locations of the four shrines. In order to activate the shrines simultaneously, the party splits into four groups. When the shrines are unlocked, the path to Terra activates. Inside Terra, Zidane and his party come across a town named Bran Bal, The party meet a female Genome named Mikoto who tells them that Bran Bal is where Garland created the Genomes Zidane and Kuja, and that Kuja keeps his tail hidden from view.
Zidane decides to find the truth of his origin in Garnet's lair, Pandemonium. After Garland attempts to isolate Zidane, the rest of the party arrives. Zidane leads the party to the top of the castle, where they defeat Kuja's dragon, Garland, and Kuja. Garland tells Kuja that he was a limited creation, and that Zidane was the true heir. Outraged, Kuja permanently trances and destroys Terra, but not before the party escapes with the Genomes. When the party returns to Gaia, they find it covered in mist.
Disc four
Kuja's final plan
They party takes the Invincible to Black Mage Village, where they drop off the Genomes and head for a purple orb above the Iifa Tree, a place called Memoria. When trying to access Memoria, a fleet of Silver Dragons comes from the orb above the Iifa Tree. The dragons start to fly towards the Invincible, but Beatrix and Cid arrive with two airship fleets. The air armadas destroy the Silver Dragons while the party enters Memoria.
Once in Memoria, Zidane hears Garland's voice, and explains to Zidane that Memoria is the resting place for all memories. After listening, the party heads up to Memoria. Once there, they travel through several forms of memories. Garland explains that everyone's memories are linked in some way. Eventually the party reaches the Crystal World, where Kuja is examining a crystal. He explains to the party that because he was a failure, he plans on destroying the crystal, which, in turn, will destroy all life. After a skirmish, Kuja unleashses an attack that injures the crystal, the party, and himself. The destruction of the crystal leads to the rise of Necron, who is the being that will destroy existance. However, Zidane urges that willpower will trumph. In order to fight Necron, half of the party transfers their life energy to the other half. The four remaining characters are teleported into Necron's lair. After an intense battle, Necron has is destroyed. As a final gasp of power, Necron initiates the destruction of the Iifa Tree.
Ending
Now on Gaia, the party appears outside of the Iifa Tree where an airship is waiting to pick them up. Zidane tells the rest of the party that he has to go into the Iifa Tree and save Kuja, and so they leave Zidane behind. Zidane manages to reach Kuja through the chaos, and the brothers forgive each other. However, Kuja soon dies, and Zidane appears to be trapped.
Meanwhile, the airship that the rest of the party boarded has dropped the party off at a repaired Alexandria. Several months pass:
Vivi: Vivi's fate remains questioned. He reproduced several versions of himself (about 5 or 6), so there are still black mages that look exactly like him. They all live in Alexandria. Many speculate that Vivi died after this, but it cannot be confirmed as it is possible that one of the black mages could have been Vivi.
Freya: Freya is at home in Burmecia where she is enjoying her life now with her long lost love, Sir Fratley.
Amarant: Amarant appears traveling with Lani through South Gate towards Alexandria, and his personality has appeared to be more accepting for his newfound friends.
Quina: Quina has become the head chef at Alexandria Castle.
Eiko: Eiko lives with Regent Cid and Hilda in Lindblum. They appear traveling to their airship to head to Alexandria.
Garnet & Steiner: Both Garnet & Steiner hold their original positions back at Alexandria. Garnet is the queen while Steiner is the head of the Knights of Pluto.
Beatrix: Beatrix is shown as a head guard at Alexandria, working alongside Steiner.
All of the party members show up in Alexandria ready to watch a Tantalus' version of "I Want to be your Canary", minus the kidnapping. The play shows the character Marcus (the character in the play, not the member of Tantalus) in a brown cloak. Near the end of the play he throws off the cloak and shouts to Garnet (who is watching on a balcony) to come down to the stage. When Marcus threw off his cloak, it was revealed to be Zidane playing the part. Garnet runs down to Zidane but drops her pendant. Believing that Zidane is far more important, she leaves the pendant behind and runs up to Zidane and hugs him. She pounds on his chest in exasperation, but they continue to stand there as the crowd cheers. Steiner and Beatrix raise a sword into the air as the sun reflects off of it, thus ending the game.