"Apocalypse Zero" is a dark and violent anime series set in a dystopian future where humanity faces extinction due to the rise of monstrous creatures known as the "Messiahs." The story centers on Kakugo Hagakure, a stoic and highly skilled warrior, and his sister, Daruga Hagakure, who possess unique abilities to combat the Messiahs. Kakugo wields the powerful "Apocalypse Zero" armor, a biomechanical suit that grants him immense strength and regenerative capabilities, while Daruga transforms into a monstrous, insect-like creature to fight alongside her brother.

The narrative begins with the siblings being summoned by their father, Dr. Hagakure, a scientist who created the Messiahs as part of a failed experiment to enhance human evolution. The Messiahs, now uncontrollable, have overrun the world, and Kakugo and Daruga are humanity's last hope. As they battle the Messiahs, they uncover disturbing truths about their origins and the extent of their father's involvement in the catastrophe. The series explores themes of survival, sacrifice, and the blurred line between humanity and monstrosity.

Throughout the series, Kakugo and Daruga face numerous adversaries, including other humans who have been transformed into Messiahs or who seek to exploit the chaos for their own gain. The siblings' relationship is a central focus, with Daruga's monstrous form serving as a constant reminder of the cost of their fight. The story delves into their psychological struggles, particularly Kakugo's internal conflict over his role as a protector and his growing detachment from humanity.

The plot is driven by intense action sequences and graphic depictions of violence, reflecting the grim tone of the series. As Kakugo and Daruga progress in their mission, they encounter a variety of characters, each with their own motivations and connections to the Messiahs. The narrative builds toward a climactic confrontation with their father, who reveals the full scope of his plans and the true nature of the Messiahs. The series concludes with a resolution that underscores the tragic and cyclical nature of the conflict, leaving the fate of humanity uncertain.