After his legendary battle against his father Yujiro Hanma ends in a draw, Baki Hanma and the other warriors of the underground arena find themselves in a state of restless boredom, having no worthy opponents left to challenge their strength. This stagnation is disrupted by Mitsunari Tokugawa, who oversees an unprecedented scientific experiment deep underground: the successful resurrection of Miyamoto Musashi, the legendary swordsman of the Edo period, through cloning and spiritual techniques. The revived Musashi, possessing the appearance, memories, and lethal combat instincts of the historical figure, quickly proves to be an anomaly from another era. He struggles to assimilate into modern Japan, clinging to ancient ideals where a duel is a matter of life and death, a philosophy that clashes violently with the present day. The central conflict ignites as this peerless samurai, wielding real blades, sets out to test his strength against the strongest fighters of the modern age.

The narrative follows a series of escalating confrontations as Musashi carves a path through the cast of iconic martial artists. One of the first to step forward is the karate master Doppo Orochi, who demands that Musashi use a real sword, leading to a brutal encounter with God's Hand. He is followed by the jujutsu master Goki Shibukawa and eventually the yakuza boss Kaoru Hanayama. A major narrative arc features the Chinese kenpo master Kaioh Retsu, who undergoes intensive training under the Sea Emperor Kaku to master a secret technique called Xiaoli specifically to counter the swordsman. Their fight concludes in a devastatingly brutal deathmatch with tragic results for Retsu. As Musashi demonstrates his supernatural ability, including a psychic sword strike known as the Imitation Cut, he attracts the attention of the most dangerous creature on the planet, Yujiro Hanma. Their clash serves as the climax of the first major story arc, where Musashi's ultimate technique proves ineffective against the reality-grounded power of Baki's father, leaving the samurai with a damaged ego and an even more dangerous mindset for the battles to come. The season also introduces the potential return of the prehistoric fighter Pickle, setting the stage for future conflicts.

BAKI-DOU: The Invincible Samurai is set in modern-day Tokyo, primarily within the blood-soaked confines of Tokugawa's underground arena, a venue where fights have no rules and the objective is simply to prove who is strongest. The cast is led by Baki Hanma, the champion whose unique mixed martial arts style and ability to conjure an imaginary opponent for shadowboxing have made him nearly unbeatable, though his search for purpose drives the plot. The antagonist, Musashi Miyamoto, serves as the ultimate contrast to the other fighters, as he is the only one who relies on a weapon, specifically the two-sword Niten Ichi-ryū style he created in life. The story explores the collision between modern unarmed combat and the lethal, weapon-based techniques of feudal Japan, examining how the strongest warriors of today handle a threat that fights with no regard for the rules of sport or the value of modern life.