Ken is recruited to serve as guardian of a village threatened by the Fang clan and becomes acquainted with their female leader Mamiya, who is a deadringer for Yuria. Elsewhere, a man named Rei, master of the Nanto Suichōken style, is killing numerous bandits while seeking the Man with Seven Scars.

Rei is hired by the Fang Clan to infiltrate Mamiya's village as a spy, where he meets Ken and his friends. However, he becomes attracted to Mamiya and switches sides.

When Mamiya's younger brother Ko is captured by the Fangs and publicly executed, Ken and Rei sets out to punish the ones responsible. Rei reveals his motive for searching for the Man with Seven Scars.

Ken, along with Rei and Mamiya, venture into Night Fog Valley in order to confront Boss Fang, the leader of the Fang Clan. Boss Fang orders his right-hand man to do a background check on Ken and Rei.

Ken, Rei, and Mamiya arrive at Boss Fang's lair, only to find out that the gang has tracked down and captured Airi, Rei's long-lost sister.

While pretending to be Ken's fiancee, Mamiya allows herself to be captured by Boss Fang under the condition that he releases Airi. However, Boss Fang does not keep his side of the bargain and forces Ken and Rei to fight each other for the safety of the women.

Ken and Rei defeat the Fang Clan and rescue women. After to Mamiya's village, Airi regains her eyesight and reveals that the man who kidnapped her wore a metal helmet. Elsewhere, a vicious gang leader with seven scars on his chest is terrorizing a village, claiming to be Kenshiro himself.

Kenshiro learns that Jagi, an adoptive brother who was also trained in the art of Hokuto Shinken, is trying to tarnish his reputation by committing numerous heinous acts while claiming to be him.

Enraged by the fact that his younger brother was chosen to be the heir to Hokuto Shinken, Jagi continues his rampage of destruction, destroying anyone who reminds him of Kenshiro. But when Ken finds out that Jagi isn't above using his abilities to exploit young children, he resolves that nothing will stand in the way of a long-awaited showdown with his brother.

Ken confronts his brother Jagi, who seeks vengeance against Ken, who was responsible for mutilating Jagi's head after failed attempt at killing Ken. During battle, Jagi reveals that he was the one responsible for convincing Shin to betray Ken

Ken hears rumors that one of his other Hokuto Shinken brothers Toki, a once benevolent healer, is now using his skills to experiment on people.

Ken confronts a group of hunters who were physically modified through pressure point experiments conducted on them by Toki.

Kenshiro confronts Toki in his lair at the Village of Miracles. However, Ken is unconvinced that his adversary is the real Toki, until he reveals the scar on his back, from which Toki gained while rescuing a young Kenshiro in the past.

Rei and Mamiya arrive to help Ken, revealing that Ken's adversary is not the real Toki, but a former follower of his named Amiba, who had the real Toki imprisoned. Before dying, Amiba reveals that he is following orders from a man known as "Ken-oh".

Mamiya seeks clues to Toki's whereabouts and learns that he is imprisoned at the Dungeon of Cassandra, the City of Wailing Demons.

Uighur, the Warden of Cassandra, blackmails a female prisoner named Bella, the successor of the Ranzan Kurenaiken (the Crimson Fist of Lotus Mountain) style, to kill Ken and his friends.

The trio reaches the Gates of Cassandra, where they confront the gatekeepers Raiga and Fuga, the twin successors of the Nishin Fūraiken ("Two Gods of Wind and Thunder Fist") style.

Ken challenges Uighur, the Warden of Cassandra, at the prison's courtyard.

While awaiting for Ken's return, Bat and Rin reminisce of their adventures with Ken and the people they met up until this point. Ken-Oh's Royal Guards arrive at Cassandra to regain their hold of the prisoners' morale.

Ken and his allies fight their way against Ken-oh's Royal Guards into Cassandra, where Toki awaits him.

While on their way to Mamiya's village, Ken and Toki reveal more about their past with Raoh to her and Rei, unaware that Ken-oh's Invasion Division is already attacking the village.

Ken, Toki, and Mamiya follow a trail of huge hoof prints left by Ken-oh's horse. Meanwhile, Ken-oh's Invasion Squad forces the villagers to pay tribute to him or be sacrifice, but Rin decides to stand up to them.

Rei arrives at Mamiya's village and rescues Rin. He confronts the leader of Ken-oh's Invasion Division, who tries to use Airi as a distraction. But Airi, spurred on by Rin's courage, gains the strength to fight for herself again. Rei goes on to defeat the Division leader, only to come face to face with none other than Ken-oh himself.

Rei challenges Ken-oh, but proves to be no match against him and is mortally wounded. Kenshiro, unable to save Rei, challenges Raoh himself, but even he too has difficulty defeating him.

Toki arrives at the village and interferes with Ken and Raoh's fight, revealing that Raoh was responsible for the death of their adoptive father Ryuken. Believing that Ken is not ready to fight Raoh, he paralyzes Ken and challenges Raoh himself.

Raoh gains the upper hand on Toki, but Ken breaks free of Toki's pressure point and challenges Raoh again. The two fight each to the point where they're both too wounded to continue, ending the battle in a stalemate.

As a result of his injury, Rei is left with only three days to live and symptoms of disfigurement are starting to show. Mamiya ventures into Medicine City by herself to search for a medicine to ease Rei's pain.

Mamiya is captured by Galf, the ruler of Medicine City. Ken and Rei rescue her, only to discover the "UD" mark tattooed behind her shoulder.

Ken and Rei learn that Mamiya was once kidnapped by a man named Yuda, who also murdered her parents. Rei reveals that Yuda is in fact, one of the Six Sacred Fists of Nanto along with Rei himself and the already deceased Shin. Ken and Rei head to Yuda's castle to confront him, but they only find his lieutenant Dagarl, who tells that Yuda has gone to the village of Blue Town.

Ken and Rei arrive at Blue Town assist a young group of rebels seeking to rescue their female friends and family from Yuda. However, the "Yuda" at Blue Town is actually a decoy. The real Yuda is revealed to had been hiding in his castle all along.

Ken and Rei return to Mamiya's village, with Rei at the verge of death. Toki offers to push a pressure point on Rei's body that will grant strength and increase his lifespan for another day, but the expense of great pain.

Yuda and his gang arrive at the village and takes Mamiya captive in order to challenge Rei to a match. Yuda reveals that he has harbored resentment towards Rei ever since they've trained together, due to the fact that Rei's graceful Nanto Suichōken is more admired than Yuda's own Nanto Kōkakuken style.

Yuda's henchmen causes a flood in the village that makes Rei stuck to the ground, giving Yuda a slight upper hand. However, Rei overcomes this and defeats Yuda with his ultimate technique. Yuda accepts his defeat and recognizes Rei as a stronger and more beautiful man. Yuda dies, but Rei himself does not have much time to live either.

In his last moment of life, Rei secludes himself from his family and friends and reminisces his adventures with Ken and co. while awaiting death. After dying, Ken cremates his body by burning the cabin with his body still in it.