"The Darwin Incident" is a science fiction anime series set in a near-future world where humanity faces the consequences of rapid technological advancement and environmental degradation. The story centers on the discovery of a mysterious phenomenon known as the "Darwin Incident," which involves the sudden emergence of a new species of highly intelligent, humanoid creatures. These beings, referred to as "Neo-Humans," possess advanced cognitive abilities and physical traits that surpass those of ordinary humans, raising questions about their origins and purpose.

The narrative unfolds through the perspectives of multiple characters, including Dr. Akira Tachibana, a geneticist who becomes deeply involved in researching the Neo-Humans. Akira's work brings her into conflict with government agencies and corporate entities seeking to exploit the Neo-Humans for their own agendas. Alongside Akira is Renjiro Kato, a journalist determined to uncover the truth behind the Darwin Incident, and Shizuka Hoshino, a young woman who forms a unique bond with one of the Neo-Humans, named "Eve." Eve's existence becomes a focal point of the story, as her abilities and connection to humanity challenge societal norms and ethical boundaries.

As the series progresses, tensions escalate between humans and Neo-Humans, leading to political intrigue, moral dilemmas, and conflicts over coexistence. The plot explores themes of evolution, identity, and the ethical implications of genetic engineering, while delving into the personal struggles of the characters as they navigate a world on the brink of transformation. The Darwin Incident serves as both a catalyst for societal change and a mirror reflecting humanity's fears and aspirations in the face of the unknown.