"Brain Powered" is a science fiction manga series set in a future where humanity faces existential threats from mysterious, biomechanical entities known as Orphans. These creatures emerge from the ocean depths, driven by an unknown force, and pose a significant danger to human civilization. The story centers around Yuu Isami, a young man who becomes a key figure in the conflict between humanity and the Orphans. Yuu pilots a powerful mecha called Brain Powerd, a humanoid weapon designed to combat the Orphans. These mechas are unique in that they are powered by a mysterious energy source called the Orphan Light, which is tied to the Orphans themselves.

The narrative explores the tension between two factions: the N.I.D.F. (New International Defense Force), which seeks to protect humanity by destroying the Orphans, and the Novis Noah, a massive, self-sustaining ark designed to preserve human life by escaping Earth. The Novis Noah is led by Yuu's estranged mother, Hime Utsumiya, who believes that coexistence with the Orphans is possible and that humanity must evolve to survive. Yuu, caught between these opposing ideologies, struggles to reconcile his personal feelings with his role in the conflict. His relationships with other characters, particularly his sister Kyan Kyan and fellow pilot Quon Kisaragi, add emotional depth to the story as they navigate themes of family, loyalty, and survival.

The plot delves into the origins of the Orphans and their connection to humanity, revealing that they are not merely mindless destroyers but part of a larger, enigmatic ecosystem. As the story progresses, Yuu and his allies uncover the truth about the Orphans and the Orphan Light, leading to a climactic confrontation that challenges their understanding of life, evolution, and the future of humanity. The series balances action-packed mecha battles with philosophical undertones, exploring the consequences of human ambition and the potential for coexistence with the unknown.