A year after the War of Shadows comes to an end, Archanea celebrates its victory over the Shadow Dragon Medeus with two wedding engagements. 
Hardin, the hero of Aurelis, will marry Nyna, the princess of Archanea, while Marth, prince of the newly liberated Altea, will wed the princess of Talys, Caeda. Heartened by the news, the people band together to continue rebuilding their homes and welcome a new era of peace.
But it is not to last. With Marth and Caeda's wedding on the horizon, Hardin summons Marth to assist him in quelling a rebellion in the kingdom of Grust. The insurrection is led by none other than Lorenz, Marth's sworn ally who fought by his side in the War of Shadows.
As Marth struggles to suppress his doubts and take up arms in service to Archanea, a new conflict is about to begin—one that will come to be known as the War of Heroes.

This game is composed of two parts: a retelling of the War of Shadows that occurred in Fire Emblem: Shadow Dragon & the Blade of Light, and a continuation of that story into the subsequent War of Heroes. It introduces support effects, which raise units' stats such as accuracy and evasion, as well as new classes like the dancer. Mounted units are newly forced to dismount while fighting indoors.