"Hallelujah: Unmei no Sentaku" is a science fiction anime series set in a dystopian future where humanity faces extinction due to environmental collapse and societal decay. The story revolves around a group of genetically engineered individuals known as "Evolvers," created to possess enhanced physical and mental abilities, tasked with restoring balance to the world. These Evolvers are divided into factions, each with conflicting ideologies on how to achieve humanity's survival.

The central protagonist, Kaito, is a young Evolver who initially lacks a clear sense of purpose. After discovering his latent abilities, he becomes entangled in a conflict between the two dominant factions: the Preservationists, who seek to rebuild society through strict control and order, and the Liberationists, who advocate for freedom and self-determination, even at the cost of further chaos. Kaito's journey is marked by his struggle to reconcile these opposing philosophies while uncovering the truth behind the creation of the Evolvers and the hidden agendas of those in power.

Key characters include Aya, a skilled fighter and Liberationist who becomes Kaito's ally and moral compass; Ren, a Preservationist leader whose rigid ideals clash with Kaito's growing empathy for humanity; and Dr. Saito, the enigmatic scientist responsible for the Evolvers' creation, whose motives remain ambiguous throughout the series. The narrative explores themes of free will, the ethics of genetic manipulation, and the consequences of humanity's hubris.

As the story progresses, Kaito and his companions uncover a conspiracy involving the exploitation of Evolvers as tools for control rather than saviors. The series builds toward a climactic confrontation where Kaito must decide whether to align with one faction, forge his own path, or risk everything to unite the divided world. The plot is driven by intense action sequences, moral dilemmas, and the evolving relationships between the characters, culminating in a resolution that leaves the fate of humanity and the Evolvers uncertain.