The story begins at Balamb Garden, an academy that trains mercenaries known as SeeD. Squall, along with Zell, Selphie, Quistis, and later Irvine, undertakes missions to confront the threat of Sorceress Edea, who controls the Galbadia Empire. As the plot unfolds, it is revealed that Edea is merely a pawn of Ultimecia, a witch from the future who is trying to compress time and dominate the past.

Squall develops a deep relationship with Rinoa Heartilly, a rebel who becomes a central figure in the story as she gains magical powers and becomes connected to Ultimecia. The game explores themes such as loneliness, fate, identity, and emotional maturation, with cinematic storytelling and impressive cutscenes.