Jakoh has been defeated, but Kenshiro must continue his journey when Lin is kidnapped and taken to the Kingdom of Shura, a country populated by ruthless warriors said to be the birthplace of the Hokuto, Nanto, and Gento arts. In order to reach Shura, Ken must cross the Sea of Death, the last remaining ocean on Earth.

Having been taken to Shura by the Pirate Akasachi, Ken finds a dying Falco, who has traveled ahead to rescue Lin, while Lin is captured by Shura warriors and bribed off as a bride in a tournament.

Shachi challenges General Kaizel, whose style allows him to remove an opponent's internal organs without leaving an open wound. Meanwhile, Kenshiro is taken to meet Shachi's former lover Leia, who preaches the value of love and friendship to the children of Shura.

Shachi, in his plot to manipulate Kenshiro into destroying the Rashō, the three main rulers of Shura, begins taking Lin to the castle the third ruler, Han, who also practices the Hokuto Ryūken styles.

As Kenshiro and Han begins their battle, Shachi tells Lin of how he began his Hokuto Ryūken training and the importance of Raoh's legacy to the commoners of Shura.

With rumors of Raoh's arrival to Shura spread as a result of Shachi's manipulation, Leia and her brother Tao goes to meet Jukei, the Hokuto Ryūken master who trained the three rulers and Shachi. Meanwhile, Han reveals to Kenshiro that the Kingdom of Shura is his birthplace.

Kenshiro reflects on what happened since his arrival to Shura, as false rumors of Raoh's arrival are spread thorough the Land. A group "rags" led by a follower of Raoh named Kosem begins to raid a training cap in order to save his young son Chen and other children from indoctrination, unaware that the man who arrived overseas is actually Kenshiro.

Rock, Kosem's elder son, decides to carry on Raoh's legend along with his band of six cowboys to form the new Army of Raoh.

Rock is blackmailed by Gammon, the Scorpion Shura, into defeating Kenshiro in order to save a group of captured villagers.

Hyoh, the second ruler of Shura, decides to mobilize his force, vowing to avenge Han's death. Meanwhile Rock and his men decide to challenge Hyoh's army, having learned that Hyoh is Kenshiro's biological older brother.

Jukei seeks to restore Hyoh's memories of Kenshiro as his younger brother. Meanwhile, Kaioh, the supreme ruler of Shura, kidnaps Lin.

Jukei and Hyoh do battle. Kenshiro battles a squad of Shura warriors on his way to Kaioh's castle, where Lin is being held captive.

Hyoh's battle with Jukei draws to a climactic conclusion as Jukei fails to restore Hyoh's memories, realizing that the seal put on Hyoh's memories was not his own, but Kaioh's. At the same time, Kenshiro is defeated by Kaioh and is taken captive.

After defeating Kenshiro, Kaioh plans on crucifying him in order to put an end to the Hokuto Shinken lineage. However,the plan falls through when Akashachi and his band of pirates come to Kenshiro's rescue. Shachi is revealed to be Akashachi's long lost son.

Following his father's death, Shachi attempts to escape with an unconscious Kenshiro while Akashachi's surviving men create a diversion to distract Kaioh.

Lin meets Sayaka, Kaioh's sister and Hyoh's fiance, who hopes that someday Hyoh will bring peace to Shura and they will cross the sea together. Elsewhere, Shahci attempts to bring Kenshiro to safety when he has a chance encounter with Hyoh which results in Shachi sacrificing his own left eye as an offering for mercy.

Kenshiro awakens at last when Cain, a Shura who seeks to succeeds the deceased Han as the third general, attacks at the waterfall. Meanwhile, Kaioh kills Sayaka and frames Kenshiro for her death.

Kenshiro and Shachi go to meet up with Leia when they are confronted by a Gyoko, a morbidly obese Shura warrior who kills anyone who reminds him of his obesity. During this battle, Kenshiro declares war on Kaioh and all who side with him. At Sayaka's funereal pyre, Hyoh pledges eternal allegiance to Kaioh.

Kenshiro and Shachi are taken in by Nagato, Hyoh's former right hand man, who turns against his master after he is corrupted by Kaioh's influence following Sayaka's death.

Kenshiro challenges Hyoh, now aware that they're biological brothers. Elsewhere, Hyoh is forcing slaves to work at Raseiden temple when he is confronted by Black Yaksha, a guardian of the Hokuto Sōke bloodline.

The bloody battle between Kenshiro and Hyoh continues while Shachi and Black Yaksha look on in horror. Kaioh reveals his true identity to Lin as Raoh's biological brother.

Kenshiro's battle with Hyoh reaches its climax. However, Shachi stops the fight, and Hyoh suddenly regains his childhood memories of Kenshiro. The now reconciled brothers unite to defeat Kaioh.

In the aftermath of Kenshiro and Hyoh's battle, Shachi heads to Taiseiden temple to unlock the secret that could allow Kenshiro to defeat Kaioh. Meanwhile, Kaioh heads out to the holy temple himself to kill Shachi in revenge for interfering with Kenshiro and Hyoh's mutual destructions.

In Taiseiden temple, a strange new discovery is made as Shachi makes a valiant last stand to defend Leia from Kaioh.

When he and Kenshiro meet for their last fight, Kaioh remembers the death of his mother, which drove him to abandon all love and affection.

Kaioh strikes a pressure point on Lin that causes her to fall asleep and fall in love with the first person she sees when she wakes up. Afterward, Kaioh and Kenshiro begin their final battle.

Kenshiro and Kaioh's fight goes underground where Kaioh has the upper hand in a pit full of toxic gases. Hyoh rescues Lin from Samoto, a Shura warriors who plans to make Lin his wife.

Accompanied by Black Yaksha, Hyoh is forced to fight Kaioh's elite army when Bat and the Hokuto Army arrive to assist them. Kaioh learns that he is descended from a branch of the Hokuto Sōke bloodline.

Hyoh, Bat and Rihaku bear witness to the final battle between Kenshiro and Kaioh. When Kenshiro deals the winning blow, Hyoh is given the opportunity to finish Kaioh off, but cannot bring himself to kill the man he once called brother.