The game follows Vahn, the quiet main hero, Noa, an excitable feral child and Gala, a curt Warrior Monk, on their quest to revive all ten Genesis Trees throughout Legaia in an attempt to vanquish the evil Mist in which the world has succumbed. Vahn initially thwarts the coming of the Mist into Rim Elm, his hometown, by reviving the local Genesis Tree and blending with the Ra-Seru entity “Meta”. Together they depart on a quest through Drake Kingdom that ends with them meeting Noa and her Ra-Seru companion “Terra” atop Mt. Rikuroa. They in turn chance upon the mother of Vahn’s love interest, long presumed dead, Maya, in the Biron Monastery, home of various warrior monks. There they also meet friends Gala and Songi, master teachers in the monastery. Gala joins Vahn and Noa once Songi turns on them and decides to use the powers of his Ra-Seru for evil. He defeats Gala, who in turn assimilates with the Ra-Seru “Ozma”.
The trio henceforth journey across the Sebucus Islands, reviving Genesis Trees, destroying Mist Generators and performing tasks and side quests for occassional secondary characters. They come face to face on multiple times against Songi, who progressively mutates into a massive monster, as well as the principal enforcers of the mist.
After cleansing both Drake Kingdom and the Sebucus Islands, the trio travels to Karisto Kingdom overseas. There they aid the towns of Sol and Buma by battling old crazed Gaza and defeating the Delilas Siblings and the creature Koru, respectively, who had held Buma under frostbite. With the aid of the Soren people – a race of winged humanoids – they attack Zora’s Flying Castle and manage to bring it down. They then go on to travel back in time to locate the origins of the Mist to put an end to it once and for all. On the process, they travel to the devastated city of Conkram. Noa finds out she is actually daughter to the king and queen of Conkram, and sister to Prince Cort, who, along with court members Dr. Jette, Zeto, Dohati and Zora – as well as Zora’s bodyguards, the Delilas – created a passport into the Ra-Seru netherworld and with it brought the Mist and its monsters into Legaia. Despite narrowly saving Conkram in the past and, once back to present, defeating surviving evildoers Cort and Jette, the denizens of Conkram perish under a giant Seru monster, and Noa’s parents meet their demise.
A faux ending is cut short with the coming of Songi to Rim Elm. Songi subdues Rim Elm under the power of the Sim-Seru Juggernaut, who devours all of its denizens. Although the trio manage to defeat Songi, finally bringing his death, they must still travel within Juggernaut and destroy it from its insides. The final battle takes place between Cort, who had survived the last encounter and fused with Juggernaut. The game ends with the destruction of Juggernaut, the rebirth of Cort into a baby, whom Noa takes care of, the reuniting of Mei and her mother Maya, and ultimate restoration of Rim Elm and everyone of its citizens.
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