"Kurokami" is set in a world where the flow of life energy, known as "Tera," is governed by a system that ensures balance. Each person has three doppelgangers, or "Doppeliners," spread across parallel worlds. When one dies, their Tera is redistributed among the remaining counterparts, with the strongest inheriting the most. This system is maintained by beings called "Coexistence Equilibrium Guardians," or "Tera Guardians," who ensure the balance of Tera across worlds.

The protagonist, Keita Ibuki, is a young martial artist living a relatively ordinary life until he encounters a Tera Guardian named Kuro. Kuro is a "Mototsumitama," a rare and powerful being tasked with maintaining the balance of Tera. After a tragic incident involving Keita's childhood friend, Akane, who is killed by a rogue Tera Guardian, Keita becomes entangled in the complex world of Tera and Doppeliners. He forms a contract with Kuro, binding their fates together and granting him enhanced abilities in exchange for aiding her mission.

As Keita and Kuro navigate their partnership, they face numerous adversaries, including other Tera Guardians and powerful individuals seeking to exploit the Tera system for their own gain. Among these foes is Excel, a ruthless and ambitious Tera Guardian who seeks to disrupt the balance of Tera to achieve ultimate power. The series explores themes of fate, sacrifice, and the consequences of tampering with the natural order, as Keita and Kuro confront the moral and ethical dilemmas inherent in their mission.

The narrative delves into the intricacies of the Tera system, revealing its vulnerabilities and the potential for abuse. Keita's journey is marked by personal growth and a deepening understanding of the responsibilities that come with his newfound powers. Kuro, on the other hand, grapples with her role as a Tera Guardian and the emotional toll it takes on her, particularly as her bond with Keita strengthens.

Throughout the series, the relationship between Keita and Kuro evolves from one of necessity to one of mutual respect and trust. Their interactions are characterized by a blend of camaraderie and tension, as they navigate the challenges posed by their enemies and the complexities of the Tera system. The story culminates in a climactic confrontation that tests their resolve and forces them to confront the true nature of their mission and the sacrifices required to maintain the balance of Tera.