After a long time wandering in the desert, Ken is taken prisoner while wandering into a village looking for water. There, he shares a cell with a young thief named Bato (Bart), and befriends his cell guard, an orphaned girl named Rin (Lynn). Shortly afterwards, a biker gang attacks the village and their leader Zeed takes Rin hostage. Ken breaks out of his cell and defeats Zeed, rescuing Rin. Ken leaves the village with Bato following him, while Rin stays behind.

The members of God's Army conduct a full-scale search of the oasis for Kenshiro. When the search team begins to execute random villagers to lure him, Ken allows himself to be captured in order to infiltrate their training facility. There, he faces against the army's drill instructor, the Mad Sarge.

Ken chases Jackal to the ruins of Villainy Prison, a place that used to imprison the most vicious of criminals. Hoping to defeat Ken, Jackal releases Devil's Rebirth, a giant demon-like killer who has mastered the forbidden art of the Arhat Deva Fist.

Shin gathers his entire army for a meeting as he officially declares war against Kenshiro. Barcom, the General of King's army, tells his men how Ken defeated some of Shin's best fighters. Meanwhile, Yuria recounts to Saki how she came to be Shin's captive and his rise to power.

With Southern Cross left in ruins following Barcom's revolt, Shin is left by himself in his own palace, protected by the few followers he still has left. Ken confronts Shin for the first time in a year and defeats him, only to learn that Yuria has already killed herself.

The final battle between Kenshiro and Raoh reaches its conclusion, as the two brothers exchange their final blows.