The Prince returns home to Babylon only to find the city ravaged by war. His actions in the previous game have reshaped the timeline, and the villainous Vizier, once thought gone, is alive and moving against him. When the Vizier seizes the power of the Sands of Time and turns himself into an immortal threat, the Prince is caught in the fallout and left changed by the Sands, which give rise to a cruel second personality known as the Dark Prince that whispers in his mind and periodically seizes control of his body. Struggling against this inner corruption, the Prince fights his way through the city to stop the Vizier, crossing paths with Farah, a woman who, in this altered timeline, has never met him before.