One hundred years after the events of Final Fantasy Blackmoon Prophecy, the world of Gaia has recovered from the conflict with Emperor Belmont, Malacore, and Zeul which saw a group of adventurers, today known as the Light Warriors, save the world from certain doom. Inhabitants of the former Esper World, now known as Lupin, have become accepted by the Humans of Gaia, with the two races working side by side.
Much of the world has changed greatly since the Light Warriors defeated the evil entities which threatened the world, though residual effects of the conflict continue to harm the world. The merging of Gaia and the Esper World, officially known as the Great Cataclysm, continues to have an effect on the inhabitants of the planet as various lands give way and sink into the ocean.
The former kingdom of Branch has suffered the greatest, as most of the kingdom has vanished into the ocean, which prompted ambitious rebels to rise up and take what was left of Branch, creating a new kingdom out of the ashes of the fallen one and naming it the Berona Republic after its founder, Carwen Berona.
The Crystals of Element, having since reformed since their destruction at the hands of Malacore, are believed to be all that keeps further side effects of the Great Cataclysm from occurring.
The rebuilt Lindblum Kingdom stands proudly as the world’s fastest growing economical and military force. With the fierce backing of Esperkind behind the kingdom, it appeared that nothing would disrupt the immense prosperity that Lindblum was experiencing until Esperkind suddenly turned against Lindblum. The game follows the adventures of a young Augurer (specially trained anti-Esper monster summoner) named Zephyr Highwind who is forced to abandon his simple lifestyle of looking after Winter, a white chocobo which belonged to his deceased sister Ezra. With new friends aiding him, Zephyr seeks to put an end to the rising hostilities between Lindblum and the Espers, led by Ramuh, before the conflict engulfs the entire globe.