"Mobile Suit Gundam 00 the Movie: A Wakening of the Trailblazer" is set two years after the events of the second season of "Mobile Suit Gundam 00." The story revolves around the Celestial Being organization and its Gundam Meisters as they face a new extraterrestrial threat. The movie begins with the discovery of an unidentified object approaching Earth, later revealed to be an alien life form known as the ELS (Extraterrestrial Living-metal Shapeshifters). These metallic entities possess the ability to assimilate and mimic any material they come into contact with, posing a significant danger to humanity.

The Earth Sphere Federation, now a unified global government, initially attempts to combat the ELS using conventional military forces but suffers heavy losses. Celestial Being, led by its Gundam Meisters—Setsuna F. Seiei, Lockon Stratos (Lyle Dylandy), Allelujah Haptism, and Tieria Erde—reemerges to confront the alien threat. Setsuna, now a true Innovator with enhanced abilities, takes a central role in the conflict. The Gundams, upgraded with advanced quantum brainwave systems, are humanity's best hope against the ELS.

As the battle intensifies, it becomes clear that the ELS are not inherently hostile but are attempting to communicate and understand humanity. However, their method of assimilation causes widespread destruction and fear. Setsuna, through his Innovator abilities, begins to sense the ELS's intentions and seeks a way to establish peaceful communication. The climax of the movie involves a daring plan to reach the ELS's core, located on Jupiter, where Setsuna and his Gundam, the 00 Qan[T], attempt to initiate a dialogue.

The narrative explores themes of understanding, coexistence, and the challenges of first contact with an alien species. The Gundam Meisters, along with their allies, must navigate the complexities of war, diplomacy, and the potential for mutual understanding. The movie concludes with a resolution that emphasizes the possibility of harmony between humanity and the ELS, achieved through empathy and technological advancement. The story ties together the overarching themes of the "Gundam 00" series, focusing on the evolution of humanity and the role of Celestial Being in shaping its future.