The story takes place in a high fantasy world, which contains an ethereal energy source named "mana". An ancient, technologically-advanced civilization exploited mana to construct the "Mana Fortress", a flying warship. This angered the world's gods, who sent giant beasts to war with the civilization. The conflict was globally destructive and nearly exhausted all signs of mana in the world, until a hero used the power of the Mana Sword to destroy the fortress and the civilization. The world began to recover in peace. As the game opens, an empire seeks eight Mana Seeds, which when "unsealed" will restore mana to the world and allow the empire to restore the Mana Fortress.
The three main characters do not have names in the original SNES release, though their names appear in the manual of the Japanese release; and their names were added into the game in the iOS port worldwide. In all versions, the player can choose to name the characters whatever they wish. The hero a young boy, is adopted by the Elder of Potos before the start of the game, after the boy's mother disappears. The girl is in love with a warrior named Dyluck, who was ordered by the king to attack Elinee's Castle. Angered by the king's actions and by her father's attempt to arrange her marriage to a local nobleman, she leaves the castle to save Dyluck and to accompany the hero as well.
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