Sword of Mana tells the tale of two unlikely companions, a former prisoner out for revenge and the last known girl from the Mana tribe. The two come together, despite their differences, for one very important reason: they are the only ones that can save the Mana tree.

Like in other games in the series, the player can take control of both characters (or join with another player in co-op) and participate in action-oriented battles using spells, weapons and different kinds of items.