"Gundam Seed" is set in the Cosmic Era, a future where humanity is divided between Naturals, who are unmodified humans, and Coordinators, genetically enhanced individuals. The conflict between these groups escalates into a full-scale war between the Earth Alliance, dominated by Naturals, and ZAFT (Zodiac Alliance of Freedom Treaty), a Coordinator-led organization based in space colonies. The story primarily unfolds through the perspectives of Kira Yamato, a Coordinator raised on the neutral colony of Heliopolis, and Athrun Zala, his childhood friend and a ZAFT soldier.

The narrative begins when ZAFT attacks Heliopolis to seize advanced mobile suits developed by the Earth Alliance, known as Gundams. Kira, a civilian student, inadvertently becomes the pilot of the Strike Gundam, one of these powerful machines, to protect his friends. This event thrusts him into the war, forcing him to confront his identity as a Coordinator fighting against other Coordinators. Kira joins the Earth Alliance ship Archangel, commanded by Lieutenant Murrue Ramius, and becomes a key figure in its defense against ZAFT forces.

Athrun, now a ZAFT pilot, is assigned to retrieve the stolen Gundams and eventually faces Kira in battle. Their friendship is strained by their opposing loyalties, creating a central emotional conflict in the series. As the war intensifies, both sides deploy increasingly destructive weapons, including nuclear strikes and genetically engineered soldiers. The story explores themes of identity, prejudice, and the devastating consequences of war, as characters grapple with their roles in the conflict.

Key characters include Lacus Clyne, a Coordinator idol and Athrun's fiancée, who advocates for peace, and Cagalli Yula Athha, a Natural and Kira's twin sister, who fights for Orb, a neutral nation resisting both factions. The series also delves into the motivations of secondary characters, such as Rau Le Creuset, a mysterious ZAFT commander with a personal vendetta against humanity, and Flay Allster, an Earth Alliance officer whose actions reflect the complexities of war.

The plot builds toward a climactic battle at the PLANTs, the Coordinator homeland, where the true scale of the conflict and its underlying causes are revealed. The resolution sees Kira and Athrun reconciling their differences and working together to prevent further destruction, though the war's scars remain. "Gundam Seed" combines personal drama with large-scale political and military conflicts, offering a nuanced portrayal of its characters and their struggles within a war-torn universe.