The military country of Baron is one of the strongest in the land, with a proud army and a majestic air force known as the Red Wings. However, the recent actions of the king make even the most loyal of his subordinates doubt his judgment. The captain of the Red Wings, Cecil, is ordered to attack the city of Mysidia and take the Water Crystal from innocent magicians who protect it. When Cecil questions the king's orders, he is immediately thrown out of the country and sent off to deliver a package to the village of Mist, accompanied by his best friend Kain, the captain of the dragoons. Little does he realize that the king's inexplicable behavior is but a part of a much larger picture, which he is yet to reveal.
The game's party system is unique in that each character belongs to a specific class, such as dragoon or white mage, with distinct special abilities or magic spells. Characters learn new abilities automatically when they reach a pre-determined level, and join and leave the party according to the game's plot events. The active party includes up to five combatants.