"Mobile Suit Gundam 00: A Wakening of the Trailblazer" is a feature-length manga adaptation of the anime film of the same name, serving as a continuation of the "Mobile Suit Gundam 00" television series. Set two years after the events of the second season, the story explores humanity's first encounter with an extraterrestrial intelligence, the ELS (Extraterrestrial Living-metal Shapeshifters), and the ensuing conflict that threatens the survival of both species.

The narrative begins with the discovery of a massive metallic object near Jupiter, identified as an alien life form. The ELS, capable of assimilating and mimicking technology and organic matter, quickly become a global threat as they advance toward Earth. The Celestial Being organization, now reformed and operating under the Earth Sphere Federation, mobilizes its Gundam Meisters—Setsuna F. Seiei, Lockon Stratos (Lyle Dylandy), Allelujah Haptism, and Tieria Erde—to confront the alien menace. The Gundams, upgraded with new technologies, are humanity's primary defense against the ELS.

Setsuna, the central protagonist, plays a pivotal role as he discovers a unique connection to the ELS through his Quantum Brainwave abilities, which allow him to perceive their intentions. This connection becomes crucial as the story progresses, revealing that the ELS are not inherently hostile but are attempting to communicate and understand humanity. The conflict escalates as the ELS begin assimilating human technology and individuals, including Innovators like Tieria, who sacrifices himself to aid Setsuna in bridging the gap between species.

The Earth Sphere Federation initially responds with military force, but their efforts prove ineffective against the ELS's adaptive capabilities. The narrative emphasizes themes of misunderstanding, communication, and coexistence, as the characters grapple with the ethical implications of their actions. The climax centers on Setsuna's transformation into a True Innovator, enabling him to establish a telepathic link with the ELS and broker peace. The resolution sees humanity and the ELS achieving mutual understanding, with the ELS integrating into human society and technology.

Key characters include Setsuna, whose journey from a child soldier to a bridge between species drives the narrative; Tieria, whose sacrifice underscores the cost of peace; and Marina Ismail, who represents the human desire for harmony. The story also explores the dynamics between the Gundam Meisters and their evolving roles in a world facing an unprecedented existential threat. The manga adaptation retains the core themes and plot of the anime film, offering a detailed exploration of the characters' struggles and the broader implications of humanity's first contact with an alien species.