"Baboo Factory" is a science fiction anime series set in a dystopian future where humanity relies on advanced biotechnology for survival. The story unfolds in a sprawling metropolis dominated by the titular Baboo Factory, a massive industrial complex that produces genetically engineered creatures called "Baboos." These creatures are designed to serve various purposes, from labor to companionship, but their creation and control have sparked ethical debates and societal unrest.

The protagonist, Kaito, is a young engineer working at the Baboo Factory. His life takes a dramatic turn when he discovers a hidden defect in the latest batch of Baboos, causing them to develop sentience and emotions. This revelation challenges the factory's rigid hierarchy and the government's strict regulations on biotechnology. Kaito forms an unlikely alliance with a sentient Baboo named Lumi, who becomes a central figure in the struggle for autonomy and rights for engineered beings.

As Kaito and Lumi navigate the factory's labyrinthine corridors, they uncover a conspiracy involving the factory's upper management and a shadowy organization seeking to exploit the Baboos for military purposes. The narrative explores themes of identity, freedom, and the moral implications of creating life. Supporting characters include Rina, a fellow engineer with a hidden agenda, and Dr. Haruto, a scientist who questions the ethical boundaries of their work.

The plot intensifies as Kaito and his allies rally a group of sentient Baboos to resist their oppressors, leading to a climactic confrontation that tests their resolve and reshapes the future of their world. The series balances action, intrigue, and philosophical inquiry, presenting a thought-provoking exploration of humanity's relationship with technology and artificial life.