In a post-apocalyptic world, the sky has turned into a mirror-like barrier following a catastrophic event known as the "Twin X" incident, which destroyed much of civilization. The story centers on two siblings, Tatsuya and Kiyoko Madoka, who are orphaned after their mother, a scientist involved in the Twin X project, commits suicide. The siblings are taken in by a mysterious organization called Orga, which operates from a secluded mansion. Orga is led by a group of enigmatic individuals who possess supernatural abilities, including telekinesis and mind control, granted by the Twin X event. These individuals, known as the "Children of Gilgamesh," are both revered and feared for their powers.

Tatsuya and Kiyoko become entangled in the conflict between Orga and a rival faction called the Countess, which seeks to exploit the Children of Gilgamesh for their own purposes. The Countess, a powerful and manipulative figure, aims to use the Children to reshape the world according to her vision. As the siblings navigate this dangerous landscape, they uncover dark secrets about their mother’s involvement in the Twin X project and the true nature of the Children of Gilgamesh. Tatsuya, in particular, struggles with his growing connection to the Children and the moral dilemmas posed by their powers.

The narrative explores themes of survival, power, and the consequences of scientific experimentation. Key characters include Tatsuya, who evolves from a protective older brother to a conflicted figure grappling with his role in the conflict; Kiyoko, whose innocence and vulnerability contrast with the harsh realities of their world; and the enigmatic leaders of Orga, such as the stoic Enkidu and the charismatic Mardina. The Countess serves as a formidable antagonist, embodying the dangers of unchecked ambition and manipulation.

The series builds toward a climactic confrontation between Orga and the Countess, with the fate of the world hanging in the balance. The resolution of the story ties together the mysteries of the Twin X incident, the origins of the Children of Gilgamesh, and the personal journeys of Tatsuya and Kiyoko. The narrative concludes with a reflection on the cost of power and the possibility of redemption in a fractured world.