Gaia, a young planet with a violent history. Many eons ago, another planet known as Terra, attempted to assimilate with Gaia. The failed assimilation annihilated what small civilizations had formed and ravaged the young planet. Many Terran structures had shifted from Terra to Gaia, along with Terra's red moon. The planet itself had become trapped inside of Gaia.

As Gaia recovered, civilizations began to rise again. A strange sheet of Mist had begun spreading across the planet, spawning ferocious monsters. As the cities of man grew, so did their thirst for power. Wars were waged for decades, but after many years of bloody conflict, there was peace among the kingdoms.

The peace was not meant to last. Brahne, the Queen of Alexandria, had begun a new war amongst the neighboring Kingdoms. A young thief named Zidane, the Queen's own daughter; Garnet, and their friends attempted to stop Queen Brahne's conquest, only to discover that she was merely a puppet being manipulated by a man named Kuja. During an intense battle between Brahne and Kuja, the queen was slain, and Princess Garnet became Queen Garnet of Alexandria. Her rule of Alexandria was short lived, as the kingdom is destroyed by monsters and a beam of light from the sky.

Zidane and his friends pursued Kuja, who was behind the attack on Alexandria. The party finally chases Kuja to Terra, his own planet, where Zidane meets a man named Garland, who reveas to Zidane the dark history of the two planets, and that he and Kuja are brothers. Zidane and his friends fight Garland, but Kuja intervenes and invokes the power of Trance, effortlessly defeating Zidane and his friends. Kuja then proceeds to kill Garland, but death does not stop Garland from informing Kuja that he will soon die. Enraged, Kuja begins to destroy everything in his sights, including the planet itself. The heroes escape the carnage, rescuing as many Genomes, the people of Terra, as they could before returning to Gaia.

Zidane and his companions confront Kuja one final time, only for Kuja to overpower them once again, using all his energy to defeat the group. However, one final battle presents itself as a being calling itself Necron, appears before Zidane, expressing its desire to end all existence. The party musters up what strength they have left to defeat Necron, and are unexpectedly whisked away by Kuja, who wished to save them from deteriorating along with Necron.

Outside of the final battleground, the great Iifa Tree, Zidane remains behind to find Kuja amongst the massive roots, while his friends return to Alexandria. As Zidane finds a Kuja, regretful and dying, the now rampant roots come crashing down upon the two.

Almost a year after the final conflict, the now rebuilt kingdom of Alexandria is celebrating Queen Garnet's seventeenth birthday. As the queen, her citizens, and the friends she had fought alongside of watch the queen's favorite play, one of the actors throws off his cloak to reveal he is none other than Zidane. Garnet and Zidane embrace each other as their friends rejoice.

It has been two weeks since Zidane's return. While Garnet attempted to govern her people, Zidane begins to frequently leave Alexandria without a word. Although Zidane always returns before the day ends, Garnet's frustration with his constant departures start to become more and more evident.