After defeating his father, Yujiro Hanma, in the greatest father-son battle on earth, Baki Hanma finds himself in a state of restless boredom. Having proven himself against the most dangerous creatures on the planet, he now yawns his way through matches in the underground arena, as no opponent can provide him with a real challenge. His fellow martial artists share this listless emptiness, going through the motions of training without their former fire.

The solution to this existential rut arrives in the most bizarre fashion imaginable. Mitsunari Tokugawa, the wealthy patron of the underground arena, finances a secret experiment deep beneath the Tokyo Skytree. Using advanced cloning technology and a spiritual ritual performed by his sister Sabuko, Tokugawa successfully resurrects Miyamoto Musashi, the most legendary swordsman in Japanese history. This peerless samurai from the Edo period is brought back to life with a single-minded purpose: to test his strength against the strongest warriors of the modern era.

Musashi is not merely a historical novelty; he is a genuine and terrifying threat. Wielding his signature two-sword style, Niten Ichi-ryu, he possesses superhuman speed and a unique ability known as the Imitation Cut, a psychic sword strike that can cut without a physical blade. More dangerous than his technique is his philosophy. Musashi clings to the ancient ideals of honor and dueling to the death, a brutal code that clashes violently with the relatively peaceful present. His arrival upends the rules of the underground arena, where the use of weapons is now permitted against this master swordsman.

The series follows a dramatic arc as Musashi systematically challenges the strongest fighters in Tokyo. One by one, legends step forward to face him. Doppo Orochi, the God of Karate, tests his fists against Musashi's steel. Goki Shibukawa attempts to use the softness of his Aiki technique to redirect the samurai's devastating cuts. The most significant early confrontation occurs when Sea King Retsu, a master of Chinese Kenpo, faces Musashi in a brutal deathmatch that pushes both fighters to their absolute limits and ends in shocking tragedy. Throughout these battles, Musashi struggles to adapt to modern society, often reacting to unfamiliar situations with lethal force, such as a gory encounter with police officers that director Toshiki Hirano describes as a horror sequence.

The first part of the series builds toward the inevitable clash between the resurrected samurai and the two pillars of the Hanma family. Baki, who finds his fighting spirit reignited by the challenge, steps forward to confront Musashi, unleashing his fastest strikes only to find the swordsman faster. However, it is Yujiro Hanma, the strongest creature on earth, who provides the ultimate test. In a highly anticipated showdown, Musashi's psychic sword strike fails to affect Yujiro, who is firmly grounded in the reality of the moment. While no official winner is declared, Yujiro's dominance leaves Musashi with a damaged ego, setting the stage for a more dangerous and focused antagonist in the second part. The finale also teases the return of Pickle, a primal prehistoric fighter, who is poised to face Musashi in a battle between two warriors living outside of their original time periods.