One hundred years after the events of 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.

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.