In ancient times, ​humanity saved the continent of Magvel from the threat of monsters by sealing evil away in five Sacred Stones. In the 800 years since then, these stones have become symbols of peace, national treasures of every country in the land.
But this age of peace is threatened as the Grado Empire, the most powerful nation on Magvel, suddenly launches surprise attacks against all of its neighbors. The kingdom of Renais, once Grado's closest ally, is taken off guard by the invasions. Unable to mount a solid resistance or counterattack, Renais can only watch as its strategic positions fall one after another. As the castle comes under attack, Fado, king of Renais, secures the safe passage of his daughter, Eirika, and then resolves to defend it to the last man.
His brave resistance is crushed, however—and with Renais fallen to ruin, it is up to Eirika, her faithful knight Seth, and a handful of her retainers to set things right. After escaping to the kingdom of Frelia, Eirika decides to venture into Grado to search for her brother, Prince Ephraim, from whom she has not heard since before the attacks began.

This game offers players a key choice at a certain point to follow one of two protagonists, Eirika or Ephraim, with the resulting story changing based on that choice. Players can now repeat extra battles on the world map, allowing them to train up their units at their leisure. Certain classes have multiple options for promotion, adding a new layer of strategic depth to character progression.