Two years have passed since the death of the New-Type Amazon Chihiro, and the world has entered an uneasy quiet. The extermination of Amazons continues under the authority of the 4C, a state-run task force. Only two original Amazons are confirmed to remain alive: the reluctant protector Haruka Mizusawa, who transforms into Kamen Rider Amazon Omega, and the genocidal hunter Jin Takayama, Kamen Rider Amazon Alpha, who has been missing for years.

The story follows Haruka, who is hunted relentlessly by a 4C squad led by the cold operative Takeshi Kurosaki. During a fierce pursuit, he is rescued by his estranged adoptive sister, Mizuki Mizusawa, a 4C member who still believes in his humanity. As they escape, the pair is discovered by a group of mysterious children and taken to a remote, idyllic facility called the Kiriko Garden, run by the charismatic director Einosuke Mido.

Haruka and Mizuki are offered refuge, but they quickly sense something wrong. The children living in the garden refer to themselves as angels destined to bring happiness. Haruka soon uncovers the horrific truth: the Kiriko Garden is not an orphanage but a farm. Under the direction of 4C chief Yugo Tachibana and Director Mido, these children are Domesticated Amazons, specifically bred to be docile, humanoid livestock for human consumption. Mido himself is an Amazon who can transform into the powerful Kamen Rider Amazon Neo Alfa, a servant of the human establishment who believes his kind can only survive as cattle.

The conflict deepens with the discovery of a chained, emaciated figure in the garden’s basement: Jin Takayama. 4C has been harvesting Jin’s Amazon cells to create the domestic breed. Upon escaping, the wild and battle-hardened Jin resumes his original mission: to exterminate every Amazon, including the innocent children of Kiriko Garden, whom he views as an abomination against the natural order.

As the facility collapses into chaos, Haruka and Jin are forced into their final confrontation. Jin argues for absolute extinction, believing any Amazon is a potential predator. Haruka, who has never eaten human flesh, argues for the right of the children to choose their own fate, even if that choice is to live. The battle is brutal and fatal. Haruka, mortally wounded, is forced to break his moral code to survive, consuming a dying child named Muku to heal himself.

In the aftermath, Jin is killed, bringing his violent crusade to an end. The livestock project is exposed, and the surviving children are freed from their cages. However, Haruka is consumed by guilt over his cannibalism. He attempts to drown himself, only to be stopped by a vision of his sister, Mizuki, who convinces him to live on as a protector for those who have nowhere else to go. As Mizuki takes over the orphanage to care for the children, Haruka watches from the shadows before disappearing into the wilderness, a monster burdened with a savior’s duty. Meanwhile, despite the exposure of the project, the 4C leadership announces a new plan, the Sigma Project, signaling that the cycle of exploiting artificial life has not ended.