"Mobile Suit Gundam 00 Special Edition" is a condensed retelling of the first season of "Mobile Suit Gundam 00," re-edited into three compilation films with additional scenes and enhanced animation. The story is set in the year 2307, where 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 and influence. Amidst this turmoil, an armed organization known as Celestial Being emerges, aiming to eradicate war through armed intervention using advanced mobile suits called Gundams.

Celestial Being's Gundam Meisters—Setsuna F. Seiei, Lockon Stratos, Allelujah Haptism, and Tieria Erde—are tasked with intervening in conflicts worldwide to suppress war and enforce peace. Setsuna, a former child soldier, pilots the Gundam Exia and is driven by a desire to end war. Lockon, the team's sharpshooter, operates the Dynames and seeks justice for his family's tragic past. Allelujah, a superhuman with a split personality, controls the Kyrios, while Tieria, a mysterious and stoic figure, commands the Virtue. Together, they challenge the world's power structures, drawing the ire of nations and private military organizations.

As Celestial Being's interventions escalate, the world's factions unite to form the United Nations Forces, aiming to counter the organization's influence. The Gundam Meisters face increasingly formidable opponents, including skilled pilots like Graham Aker of the Union and Sergei Smirnov of the Human Reform League. The conflict intensifies with the introduction of the Thrones, a rogue faction of Gundams operating independently of Celestial Being, whose brutal methods undermine the organization's goals. The Thrones' actions lead to widespread backlash, forcing Celestial Being into a precarious position.

The narrative explores themes of idealism, the ethics of intervention, and the cyclical nature of conflict. Celestial Being's mission is tested as their actions inadvertently fuel greater hostilities, raising questions about the feasibility of their goal. The story delves into the personal struggles of the Gundam Meisters, particularly Setsuna, whose past as a child soldier shapes his worldview and determination. The series also introduces Aeolia Schenberg, the enigmatic founder of Celestial Being, whose long-term vision for humanity's future remains shrouded in mystery.

The Special Edition condenses the original 25-episode season into a more streamlined format, retaining key plot points and character development while enhancing the visual presentation. It serves as an accessible entry point for newcomers and a refresher for returning viewers, capturing the essence of the series' political intrigue, intense mecha battles, and philosophical undertones. The story concludes with Celestial Being facing overwhelming odds, setting the stage for the second season's continuation of the conflict and the evolution of its characters.