Three years have passed since the Daein-Crimea war, where the mercenary Ike led the Crimean army to defeat Daein's mad King Ashnard. Both Daein and Crimea are still stabilizing after that war. Daein is ruled by the Begnion occupation forces, after Crimea relinquished rule over their defeated country, and they are oppressed by the imperial soldiers. In the first of the game's four parts, a group of chivalrous thieves, which includes fortune-teller Micaiah, fight Begnion's oppression and attempt to liberate Daein and bring back power to the royal family.
The efforts of the Dawn Brigade are the beginning of a much larger conflict. In the next part, Crimea's Queen Elincia fights against conspiring nobles, who plot to overthrow her. The following part sees the Greil mercenaries assist the united Laguz army as they go to war with the Begnion Empire. The consequences of this war can be seen in the fourth and final part, where the Dawn Brigade and the Greil mercenaries join forces to defeat the Begnion senate and the threatening goddess of chaos high above at the Guiding Tower.