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Kuja is the main antagonist of Final Fantasy IX. He is known for his long, white locks, and rather flamboyant style of dress. His effeminate looks are deceiving, however, as he holds tremendous power.
He is a sinister man, while not overtly insane, his twisted sense of humor and tendency towards violent, sadistic behavior make him a force to be reckoned with. He's a severe egomaniac, who can't even handle his own mortality and vows to take down all life with his own.
 

Background

Kuja is a genome, created by Garland on the planet Terra. Kuja was to be an "Angel of Death", but Garland made him to have only a limited lifespan (in essence, Kuja was ironically akin to Vivi, in that he was a prototype with a limited lifespan). He would ultimately be replaced by Garland's second, more improved genome, Zidane. Kuja, feeling threatened by Zidane, cast him off onto Gaia, hoping to kill him. This did not occur, however, unbeknownst to Kuja.
As time went by, Kuja began fulfilling his purpose as an Angel of Death, though his intention was to manipulate the situation to his advantage. He started fueling wars, using Mist to manufacture violent soldiers and beasts to aid him and those he supplied with power. 

Story

Kuja is first seen in FFIX when Zidane and Freya are spying on Queen Brahne in Burmecia. He approaches, enjoying the rain as something of a victory downpour. After the battle with Beatrix, Freya briefly witnesses Kuja get onto his Silver Dragon (the creature that helps identify Kuja throughout the game), and fly away into the sky. 
It is learned from the team that Kuja is the one responsible for the manufacturing of Black Mages in Dali, having provided the recipe and magic to supply Queen Brahne with an army; and Mistodons: undead, worm-like beasts with high HP and strength stats. Both creatures are major enemies throughout a large portion of the game.
He is next seen by Garnet in Treno, where he is at the Auction house. He is seen in an ATE talking to the Auctioneer as an underling, leading some to believe he is the mysterious "King" in Treno. While there is much evidence to suggest this, it is never confirmed.
As Garnet arrives in Alexandria and is talking with her mother, Kuja walks in. With his magic, he puts her into a deep sleep, where his minions Zorn and Thorn can then extract her Eidolons. It is because of him that Cleyra, Burmecia, and Lindblum get nearly destroyed, and the party arrives in Lindblum intent on stopping him. They hatch a plan to head to the Outer Continent, where Kuja is believed to be residing, in an effort to stop him, and ultimately stop the production of his blood-thirsty Black Mages.
This leads the team to the Iifa Tree, where, it is learned, Kuja is getting his Mist for manufacture. It is here that Kuja unleashes his next piece of arsenal, the hyper advanced airship Invincible. Using its powers, he seduces Bahamut to his side, who then obliterates the Alexandrian ship fleet and kills Queen Brahne, who was attempting to kill Kuja and take over all the power over Gaia. It soon becomes apparent Kuja is the real enemy, not Brahne, and from then on he becomes the team's sole target, for both revenge for Brahne's death and the safety of the rest of the Gaians.
Kuja next sets his eyes on Alexandria, intending to prey on their fragility with a new Queen and weakened army. He calls, through the Invincible, Bahamut, who begins to ravage the city. Mysteriously, Eiko and Garnet combine their sacred jewels to summon the holy Eidolon Alexander, who makes dragon meat of Bahamut. Kuja attempts to obtain Alexander with Invincible, but Garland, a mysterious old man, instead kills Alexander, preventing Kuja from obtaining the most powerful Eidolon. It is after this point that the group learns Kuja has fooled the "aware" Black Mages from the Black Mage Village into working for him, so they may extend their lifespans. He later reveals to the Black Mages that he couldn't extend their lives; it was a futile effort.
The team then makes their way to Kuja's Desert Palace, located on the northeastern area of the continent and hidden beneath a sandpit. Here he captures the group, splitting the party and sending Zidane on an errand to get a mysterious stone in Oeilivert. He plots to kill the remaining party members in his palace, and then Zidane's party upon their return. Zidane sees that Kuja is in control of the ship Regent Cid's wife had stolen some years earlier at this time. The other party escapes the Desert Palace, but Kuja takes the Gulug Stone from Oeilivert and Eiko as hostage. The party gives chase, leading to Mt. Gulug, where he attempts to extract Eiko's Eidolons, to no avail since she's not 16 years old yet. It is here that the party discovers Kuja had been keeping Hilda, Regent Cid's wife, captive, and she unveils a rather unbelievable story.
The team sets out to get to the other planet from which Kuja came, and they eventually do so, though unfortunately Kuja comes along for the ride, all a part of his master plan. They arrive on Terra, discovering the true purpose and past of not only Kuja, but Zidane as well. It is learned they are both Angels of Death, and that Kuja was to be replaced by Zidane. After this, Kuja went rouge, abandoning Zidane and doing things his own way.
On Terra, the party finally faces off with Kuja, and after the battle he suddenly Trances, obtaining the power he wanted since witnessing Mog's Trance into the Eidolon Madeen. In his Trance state, he uses Ultima, his best spell, which nearly kills Zidane and the team. As he gloats over his newfound powers and self-assured victory, he kills the weakened Garland. However, Garland somehow lives on, and he tells Kuja telepathically that he won't be able to use his immense strength for long, as he, like the Black Mages he created, has only a limited lifespan, and will "die" soon. In a frenzied rage, he unleashes a powerful array of attacks on his home planet, effectively destroying it just as Zidane and the party escape back to Gaia.
When back on Gaia, he sets out to destroy the Crystal, the bringer of all life and existence, since he felt that if he couldn't live forever, nobody should. The party challenges him, in the ultimate face-off, and in the end, he casts Ultima one last time, technically succeeding in his goal of eliminating all life. After the party battles with Necron to save existence, Kuja uses his last remaining Trance powers to teleport the team from Necron's explosive death, and the team leaves the Iifa Tree. Then Zidane faintly hears Kuja's voice (via telepathy), and, in an act of misunderstood brotherly love, sets out to save him. Zidane arrives to where Kuja had fallen, and he and Kuja talk, where Kuja ultimately accepts his fate and shows remorse for all his wrongdoings, something very unfamiliar in main antagonists in the Final Fantasy universe. He finally dies, no longer in his Trance form.

In the end, Kuja changes for the good, however it only happens as he arrives on death's door, and he dies while his younger brother Zidane tries to save him.
 

BATTLES


Kuja (First Fight):

HP: 42,382
AP: 0
Items: Ether; Carabini Mail; Light Robe
The first battle against Kuja isn't difficult. He uses some strong magic attacks, but nothing you can't handle. If you want, summoning Carbuncle or casting Reflect could be done. You may also wish to steal with Zidane, for the armors. Otherwise, several attacks and strong magic attacks should take him down relatively quick. He Trances at the end of this battle, and finishes the battle with an Ultima spell.
 

Trance Kuja:

HP: 55,535
AP: 0
Items: Ether; White Robe; Rebirth Ring
Like the first battle, Kuja uses strong attack spells, in particular, Flare Star (much like Flare, only stronger). He also uses Reflect, so watch out for that if you're using Vivi (or are using Eiko's 'Holy' spell). Summons work well, as do strong physical attacks. If you want to get some extra gear and items for the Necron boss fight, go ahead and steal with Zidane. Be sure to hit Kuja with all you 've got, since you will fully heal for the next boss battle right after this.
Kuja finishes this battle off with another Ultima, and the screen goes white.

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