Over thousands of years ago a planet by the name of Terra attempted a Fusion with its younger sister planet, Gaia, but was a disastrous failure and left the surface and civilizations of Gaia destroyed and in utter ruin. Terra then wraps itself inside Gaia, giving the planet its two moons and shifting many of the Terran locations onto the planet of of the people that lived on Terra took their souls to Pandemonium, a castle that belongs to a man named Garland, who is an android created by the Terrans to help them moved Terra's magical tree, the Iifa Tree, to Gaia so it could help the planet recover and heal, which would take over thousands of years.2000 years pass after the Fusion and Garland begins his construction on Genomes to serve as vessels for the sleeping Terran souls once the next Fusion was passes, people are born, events happen. Wars happen and Garland becomes frustrated for the wars on the Mist Continent ceased, which slows the pace of Gaian souls attempting to return to their crystal that lies in the heart of the chooses to create a special Genome with a mind and will of its own to insinuate the Genome was , Garland saw Kuja as a failure because he was not able to develop complex human feelings, which means he was not easy for Garland to manipulate to his will. Kuja was also unable to enter Trace, which was the world's ultimate not wanting Kuja to go to complete waste, Garland secretly gives the Genome a short lifespan while he creates another Genome, without telling years later Zidane Tribal is created with the body of a young child so he could grow and mature, and thus develop emotions naturally, and become stronger than Kuja. Kuja becomes jealous of his younger 'sibling' and plots his demise over him and four years later Kuja kidnaps Zidane and dumps him on Gaia, Garland becomes furious with Kuja in Zidane's disappearance and banishes Kuja from Terra. Kuja then makes the Desert Palace his the year of 1799, Kuja meets Queen Brahne, Queen of Alexandria, and begin to collaborate with her. Due to the fact Kuja found interest in the eidolon's power after his banishment, he influences Brahne to desire their mystic and awesome power to conquer the neighboring nations so they can obtain fragments of the crystal that holds the power of summoning Alexander, the strongest eidolon of them all. Kuja promised to aid Brahne in the schemes and to aid her in both weapon supply and in showing her how to create large numbers of Black Mages. But what Brahne didn't know was that Kuja was secretly plotting his revenge and domination over Garland. By obtaining control over the eidolon Alexander, Kuja would be powerful enough to rule both the planets of Gaia and Terra.
Very soon the neighboring kingdom of Burmecia is conquered and Kuja crosses paths with Zidane and his friends (Yet he did not recognize his younger 'sibling' at the time ) he leaves the kingdom, sparing Zidane and his companion's lives. Meanwhile Brahne , under Kuja's advice, extracts Garnet's, her adopted daughter and Princess of Alexandria, eidolons and uses one by the name of Odin to kill any survivors of Burmecia. Some time later Zidane and his companions interrupt Kuja's production of Black Mages by destroying their power source, a creature by the name of SoulCage, but Kuja could care the Black Mage Village, Kuja was under attack by Brahne's fleet because she found no further use for him. Kuja survives the attack and forces Brahne to summon Bahamut to try and kill him. Kuja enslaves Bahamut by using the Invincible, an airship constructed by the Terrans that is specialized for war and enslavement, and Bahamut destroys Queen Brahne's entire fleet, killing everyone on board the ships, including herself. This instantly crowns Garnet the new Queen of Alexandria, and Kuja sets forth to try and kill her as well. Kuja summons Bahamut and commands it to destroy the entire kingdom of Alexandria, however Garnet and Eiko rush to Alexandria Castle's turrets and summons the eidolon, Alexander, by combining the four crystal fragments destroys Bahamut and Kuja attempts to enslave Alexander by using the Invincible once again, but Garland was at the controls, realizing Kuja's desire to rebel. The Invincible destroys both Alexander and Alexandria, leaving Kuja with not eidolon to manipulate and he vows to find an eidolon even stronger than Alexander and flees the ruins of Kuja seized control of an airship by the name of the Hilda Garde. Zidane and his friends attempt to stop Kuja but instead Kuja captures the group and takes them all to his home on Gaia, the Desert then tells Zidane he will free his friends if Zidane gets an artefact for him. Zidane accepts and was allowed to have three of his companions join Zidane was in Oeilvert looking for the item Kuja requested, Kuja attempts to kill the remainder of Zidane's companions who were still in the Desert Palace, they all escape, and Zidane returns before Kuja finds the escapees and hand over what Kuja was looking for. The Gulug Stone from Oeilvert. Kuja escapes with Eiko, the youngest in Zidane's group and an extremely powerful summoner, Zidane follows Kuja to Mount Gulug as Zorn and Thorn, Kuja's henchmen who originally served as Queen Brahne's court jesters and mages, attempt to extract little Eiko's eidolons but failed because she was too with his master's kidnapping, Eiko's pet Moogle, Mog, enters Trance and reveals he is actually an eidolon by the name of Madeen. Kuja was amazed by this and realizes that in order to enter Trance, one must merely needs to experience a surge of powerful emotions.A new plan starts to form in Kuja's mind. He decides he doesn't need the eidolons to defeat Garland. All he needs to do is enter a Garland was off the Invincible and trying to take away Zidane's soul (which would turn him into a normal, practically mindless Genome), Kuja seizes control of the Invincible.Engaging in battle with Zidane and his friends, Kuja enters Trance and crushes them with Ultima( Which is one of the most powerful spells ever known ), and reveals that he had absorbed all of the spells on the Invincible, including the soul of Queen Brahne. It was the Queen's feelings of greed, hatred, and jealousy that allowed Kuja to enter such a powerful Trance. (Because Kuja is a Genome and was originally constructed to be a vessel for souls, he is able to absorb souls ).Kuja kicks a weakened and defeated Garland off the precipice of Castle Pandemonium and declares that he will rule both planets of Gaia and Kuja taunts the defeated Zidane, Garland's spirit speaks to Kuja and tells him that his is not immortal as he originally thought, and that he was only going to survive until the real Angel of Death, Zidane, reaches maturity. Kuja comes to realize that he is nothing more than a temporary pawn of Garland's using, this revelation drives Kuja to madness and he declares that the worlds wouldn't mean anything without his a mad rage, Kuja destroys the planet Terra and returns to Gaia. Barely escaping, Zidane and his companions ( and some Genomes they managed to rescue) return to Gaia and surmise that Kuja is at the Iifa Tree and with assistance from General Beatrix, Zidane and his friends penetrate the barrier to Memoria, a world that holds the planet's memories. Guided by Garland's spirit, they find the innermost realm of Memoria, the Crystal the Crystal World, they find Kuja at the Crystal, the source of all life. Still unwilling life to continue without himself, Kuja summons Deathguise, who is summarily destroyed (due to the fact Zidane and his friends fought him earlier on ). Kuja battles Zidane's allies himself, and upon his defeat he casts Ultima, which defeats Zidane's allies and they appears in the Hill of Despair and encounters Necron, a being who has appeared to destroy all life. Necron is defeated, and life is allowed to Necron's defeat, Kuja uses the last of his powers to teleport Zidane and his friends outside of the dying and raging Iifa Tree. Zidane decides to stay behind to try and rescue Kuja, barely making it into the Iifa Tree's core as its trunks and roots collapse, Zidane finds Kuja. Having a change of heart, Kuja tells Zidane he is sorry for al that he did, but Zidane understands why he did , the third Angel of Death Garland created after Zidane's disappearance and Kuja's banishment, tells Kuja in spirit how he taught the Genomes that they can be more than just mindless vessels and has given them hope for the future. Suddenly the Iifa Tree's interior begins to collapse and Zidane instantly shields Kuja as flailing roots converge on was never known in record if Kuja survived.
Until the Dissidia happened. The Dissidia was a great war between two gods, Chaos and is the god of Discord while Cosmos is the goddess of Harmony, they summoned warriors from many different times and worlds to do battle, Kuja was won of these summoned warriors.
Chaos, the god is Discord, summoned Kuja. He is the youngest of the villains serving Chaos and is looked down by his peers for his youth and inexperience. Determined to prove himself their superior, Kuja concocts several plans to trap the Warriors of Cosmos, particularly his younger 'brother' Zidane, with the intent to break his spirit with isolation and feelings of powerlessness. To accomplish his goals, he works alongside other Warriors of Chaos, Exdeath and Kefka Palazzo. Kuja initially plans to abduct one of Zidane's companions, Squall Leonhart, as bait. But Squall defeats Kuja in battle and Kuja changes his plans and uses a fake Crystal to kidnap Zidane directly, however another one of Zidane's friends, Bartz Klauser, takes the Crystal instead and Kuja uses him to unwittingly deliver another fake Crystal to Zidane, isolating him from his friends and leaving him to fight Kuja alone. However, sometime before this Kuja and Zidane recover all their memories and on friendly terms. Kuja plots to betray Chaos by leading Zidane, Squall and Bartz to Chaos' throne so the four of them can defeat him and end the war Palazzo finds out about this and informs Emperor Mateus and Ultimecia and they plan to ruin Kuja's goals by acting as though Kuja was luring Zidane and his friends into a trap. Seeing what Mateus, Ultimecia and Kefka were doing, Kuja quickly plays along in their lies and attacks Zidane, Squall and Bartz, but allows them to escape. Kuja is later on defeated by Lightning Farron after being goaded to challenge her by the cycles of the Dissidia, Kefka interferes with Kuja's memories, twisting and changing them to make Kuja believe Zidane to be his enemy and takes joy in seeing him suffer and to be loyal to Kuja learn that his memories have been interfered with Kuja become infuriated and vows to defeat Zidane to demonstrate that memories, true or false, are not needed to prove his worth, power, strength and intelligence.