With Rei now dead, only three of the Six Sacred Fists of Nanto remain and Kenshiro sets off to find the remaining ones. One of them, a man named Souther, has proclaimed himself to the "Holy Emperor" and seeks to conquer the world as well.
Defeated by Souther, Ken is captured so he could be used as a sacrifice for the completion of Souther's Holy Cross Mausoleum. However, Shu's young son Shiva sets off to infiltrate Souther's lair and save Ken, even at the cost of his own life.
Ken is rescued, but at the tragic cost of Shiva's life. However, with Ken still injured from his fight with Souther, Shu decides to hide him and challenges Souther for the sake of his people.
Shu is defeated by Souther and is forced to carry the stone that will serve as the summit of Souther's pyramid. Sensing Shu's struggle, Ken awakens and quickly regains his full strength.
Ken arrives at the Holy Cross Mausoleum and witnesses Shu's public execution at the hands of Souther. But before dying, Shu miraculously recovers his eyesight and sees the now grown Kenshiro before dying. Toki and Raoh also arrive at the scene to witness Ken's fight with Southeer.
Before accepting Kenshiro's challenge, Souther recites his tragic childhood and his motive for building the Holy Cross Mausoleum. Ken fights Souther again and struggles, until he finally fathoms the secret behind Souther's invulnerability.
Raoh regains his full strength and seeks Koryu, Ryuken's former rival, to test his power, while Toki, who was once willing to settle using his skills to heal the weak, has regained his determination as a martial artist.
Ryuga, who swore royalty to Raoh and his tyranny, witnesses Kenshiro's compassion to others and is determined to find out which of the two brothers is more to fit to lead the world.
While cremating Toki's and Ryuga's remains, Ken remembers where it all began - with his old nemesis Shin, the man who engraved the seven scars on his chest and once kidnapped his beloved Yuria.