"Gundam 00" is set in the year 2307 AD, a time when fossil fuels have been depleted, and humanity relies on solar power harvested by orbital elevators. Three major power blocs—the Union, the Human Reform League, and the AEU—control these elevators, leading to constant conflict over resources. Amidst this instability, a private military organization called Celestial Being emerges, armed with advanced mobile suits known as Gundams. Their mission is to eradicate war through armed intervention, targeting all factions equally to force humanity toward peace.

The story centers on the Gundam Meisters, the pilots of Celestial Being's Gundams. Setsuna F. Seiei, a former child soldier from the war-torn Middle Eastern Republic of Krugis, pilots the GN-001 Gundam Exia. He is joined by Lockon Stratos, a skilled sniper operating the GN-002 Gundam Dynames; Allelujah Haptism, a super-soldier with a split personality piloting the GN-003 Gundam Kyrios; and Tieria Erde, a mysterious and stoic individual who controls the GN-005 Gundam Virtue. Together, they carry out missions to disrupt conflicts worldwide, drawing the ire of the power blocs and sparking a global response.

As the series progresses, Celestial Being's actions lead to the formation of the United Nations Forces, a coalition aimed at countering their influence. The Gundam Meisters face increasingly formidable opponents, including Graham Aker, a Union ace pilot obsessed with defeating the Gundams, and Ali al-Saachez, a mercenary with ties to Setsuna's past. The narrative explores the ethical implications of Celestial Being's methods, as their interventions often result in collateral damage and unintended consequences.

The second season, set four years later, reveals that Celestial Being's actions have not achieved lasting peace. Instead, the world has united under the Earth Sphere Federation, but conflicts persist. A new faction, the Innovators, emerges, seeking to manipulate humanity's evolution and control the future. The Gundam Meisters, now operating upgraded Gundams, must confront this new threat while grappling with their own ideals and the consequences of their actions. The series culminates in a climactic battle that determines the fate of humanity and the future of Celestial Being's mission.

Throughout the series, themes of war, peace, and human evolution are explored through the perspectives of the Gundam Meisters and their adversaries. The narrative delves into the complexities of morality, the cost of idealism, and the cyclical nature of conflict, presenting a multifaceted portrayal of its characters and their struggles.