"Lunatan: 1-Mannen no Himitsu" centers on a young man named Lunatan, who discovers he possesses a unique ability tied to an ancient secret spanning 10,000 years. The story unfolds in a world where humanity coexists with remnants of an advanced, long-lost civilization. Lunatan’s ability allows him to access fragments of this civilization’s knowledge, granting him extraordinary powers but also making him a target for various factions seeking to exploit or destroy him.

The narrative begins with Lunatan living a seemingly ordinary life in a small village, unaware of his latent abilities. After a sudden attack by a mysterious organization, he is forced to flee, accompanied by a skilled warrior named Kaela, who reveals his connection to the ancient secret. Together, they embark on a journey to uncover the truth behind Lunatan’s powers and the civilization that left them behind. Along the way, they encounter allies and enemies, including rogue scientists, rival factions, and remnants of the ancient civilization itself.

As the story progresses, Lunatan learns that his abilities are tied to a powerful artifact known as the "Eternal Core," which holds the key to reshaping the world. The artifact’s existence sparks a global conflict, with multiple groups vying for control. Lunatan must navigate this dangerous landscape, balancing his growing powers with the moral dilemmas they present. Kaela serves as both a protector and a mentor, helping him understand the weight of his responsibilities.

The series explores themes of legacy, power, and the consequences of humanity’s pursuit of knowledge. Lunatan’s journey is marked by personal growth, as he grapples with the ethical implications of his abilities and the impact they have on those around him. The plot is driven by a mix of action, mystery, and character development, with each episode revealing new layers of the ancient secret and its connection to the present. The story builds toward a climactic confrontation, where Lunatan must decide how to use the Eternal Core and determine the fate of the world.