Three years have passed since the conflict between Daein and Crimea shook every corner of the continent of Tellius. Elincia, the orphaned heir to the throne of Crimea, is crowned queen and sets out to heal the damage her country suffered to push Daein from its borders. Daein, having lost the war, cedes its governmental authority to the Begnion Empire.
But when Begnion becomes a tyrannical suzerain, civil unrest grows by the day. Micaiah, a girl with powers of healing and foresight, joins with other young people who have escaped the empire's grasp to form the Dawn Brigade—a loose band of vigilantes intent on freeing Daein from Begnion's stranglehold. Though Micaiah's efforts earn the respect of her people, who begin to call her the Silver-Haired Maiden, she is initially unable to make much headway against Begnion's overwhelming strength.
Word soon reaches Micaiah's ears, however, that a prince—orphaned son of Daein's late King Ashnard—is raising an army in the Desert of Death with plans to lay claim to the throne. Micaiah leads the Dawn Brigade into the desert in the hopes of rallying behind Daein's rightful ruler and breaking the kingdom's shackles.

This game's story is divided into four distinct parts that alternate between two different armies, allowing players to see the story from two different perspectives. The skill system from Fire Emblem: Path of Radiance is even more flexible here, making it easier than ever to customize units by adding and removing skills.