Joe Logan is the central character of the story, a former ninja whose real name is Higan. After escaping his clan, he adopted the alias Joe Logan and sought a peaceful life in rural America, hoping to hide from his violent past. He lived with his wife, Mari or Sara, and their son, Ren, working as a farmer and striving to be a laid-back family man who cherished his quiet existence. This tranquil life, however, was shattered when his clan tracked him down and brutally murdered his wife and child, leaving Joe for dead.

Driven by a burning desire for vengeance, Joe survives his grievous wounds and emerges from his assumed death as the relentless ninja he once was. His primary motivation is to annihilate the ninja clan and its leader, Yamaji, who ordered the attack on his family. This quest transforms him from a peaceful farmer into an unstoppable force of retribution, fueled by grief and pure rage. Throughout his journey, he interacts with FBI agents Mike Moriss and Emma Samanda, who investigate the murders and become entangled in his bloody war against the clan.

Joe Logan is an exceptionally powerful and highly skilled ninja. His abilities include superhuman speed, immense strength, and masterful proficiency with bladed weapons. He is also capable of using a unique ninja art known as the Secret Stark of Awareness, which manifests as a smoke-like substance that disorients his opponents and amplifies his own powers, though using it repeatedly takes a toll on his body. His resilience is remarkable; he has been referred to as seemingly incapable of dying, able to revive himself and continue fighting even after suffering fatal wounds. As the narrative progresses, his development sees him fully reclaiming his identity as the Ninja Kamui, shedding his peaceful facade and demonstrating the full, terrifying extent of his capabilities as a warrior.