The game is set three years after the events of the first Suikoden. Riou, a young soldier in the Highland army's Unicorn Youth Brigade, and his best friend Jowy Atreides witness a false flag massacre orchestrated by the ruthless Prince Luca Blight. Forced to flee their own army, the two are separated and each comes into possession of one half of the Rune of the Beginning, a powerful True Rune that governs conflict and war. The Rune's dark fate dictates that its two bearers must eventually fight until only one remains. As a devastating war erupts between the Kingdom of Highland and the City-States of Jowston, Riou finds himself leading a growing resistance against Luca Blight's brutal campaign of conquest. With Jowy drawn deeper into Highland's political machinations and their paths diverging, Riou must recruit allies, build a stronghold, and confront the mounting cost of the conflict, all while the Rune's curse threatens to pit the two friends against each other.