The game is set on the continent of Fódlan, which is divided into three territories: the Adrestian Empire, the Holy Kingdom of Faerghus, and the Leicester Alliance. The story follows a mercenary named Byleth, who becomes a professor at the Garreg Mach Monastery, a prestigious Officers Academy that trains students from all three territories.

The player chooses one of three houses to teach at: the Black Eagles, the Blue Lions, or the Golden Deer. Each house has its own unique characters, story, and perspective on the events of the game.