"Kyukyoku Chojin R" is a science fiction anime series set in a futuristic world where humanity faces extinction due to the emergence of powerful beings known as Chojin. These superhuman entities possess extraordinary abilities and are divided into two factions: the benevolent Chojin, who seek to protect humanity, and the malevolent Chojin, who aim to dominate or destroy it. The story centers on R, a young man who becomes a Chojin after a mysterious transformation. Initially unaware of his newfound powers, R is thrust into a conflict that determines the fate of both humans and Chojin.

The narrative unfolds as R discovers his abilities and learns about the existence of other Chojin. He encounters allies such as Aya, a skilled fighter with her own Chojin powers, and Kakeru, a scientist dedicated to understanding the origins of the Chojin phenomenon. Together, they form a resistance group to combat the malevolent Chojin led by the enigmatic and ruthless leader, Zagi. Zagi seeks to harness the ultimate power of the Chojin to reshape the world according to his vision, posing a grave threat to humanity.

As the story progresses, R and his allies uncover the truth behind the Chojin's origins, which are tied to advanced genetic experiments and a hidden organization manipulating events from the shadows. The series explores themes of identity, power, and the ethical implications of genetic manipulation. R's journey is marked by internal struggles as he grapples with his dual nature as both human and Chojin, while external conflicts escalate into large-scale battles between the factions.

The plot is driven by a series of confrontations, alliances, and betrayals, culminating in a final showdown between R and Zagi. The resolution of the conflict hinges on R's ability to reconcile his humanity with his Chojin powers, ultimately determining the future of both species. The series balances action-packed sequences with moments of introspection, providing a layered exploration of its central characters and their motivations.