he game takes place in a world called Legaia, populated by humans and objects called Seru, which can join with humans to grant them fantastic powers. While humans and Seru had once peacefully coexisted, about ten years before the game begins the world was covered in a mist which drove Seru mad when it came in contact with them. Seru were transformed into monsters that attacked humans, and human civilization nearly collapsed. At the time the game begins, human survivors have banded together in remote regions to hide from the mist.

The game follows Vahn, the quiet main hero; Noa, an excitable feral child; and Gala, a curt warrior monk, on their quest to revive ten Genesis Trees throughout Legaia in an attempt to vanquish the evil Mist which covers the world. The three heroes join with entities known as Ra-Seru, which grant them powers like Seru but are immune to the effects of the Mist. They travel across three continents, reviving Genesis Trees that push back the Mist over small areas, and destroying the Mist Generators that create it; at times they come into conflict with Songi, Gala's childhood rival, who has joined with a Seru and is progressively mutating into a monster.

Towards the end of their quest, in the devastated city of Conkram, the heroes manage to travel back in time to locate the origins of the Mist to put an end to it once and for all. They discover that the Mist was created as a biological weapon by Prince Cort, Noa's brother and the prince of Conkram. They are unable to save Conkram or Noa's parents in the past, but when they return to the present they destroy the final Mist Generator and defeat Cort. Unbeknownst to the heroes, however, before dying Cort manages to merge with Juggernaut, a Seru that has grown gargantuan through exposure to the Mist.

The heroes return triumphantly to Vahn's hometown of Rim Elm, but are soon attacked by Songi and the giant Seru Juggernaut, which devours the entire town and its citizens. After defeating Songi, the heroes must travel inside Juggernaut to face and defeat Cort again. The game ends with the destruction of Juggernaut, the rebirth of Cort into a baby (who Noa takes care of), and the ultimate restoration of Rim Elm and all its citizens.