The continent of Lanzheim is thrown into chaos when the prime minister, Schuenzeit, assassinates the queen and takes the throne for himself. Princess Rzephilda organizes a resistance and civil war breaks out. The war seems to go in Rzephilda's favor, until Schuenzeit unleashes terrible abominations called Sentinels.
A young amnesiac named Juto lives a quiet life in a fishing village on Highwind Island. Everything changes when the civil war reaches the island, and he is forced into action. The player assumes the role of Juto and sees the war through to completion.