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.

Ken rescues an old man named Smith from Spade, a member of the Four Jacks working for the King organization. The old man seeks to deliver a bag of rice seeds to his village, hoping to harvest them for the future. Ken and Bato take Smith to his village, unaware that Spade and his men are following them. Spade, who lost his eye during his initial encounter with Ken, attacks the village and kills Smith in retaliation. Unable to rescue Smith, an angry Ken kills Spade with a technique that makes their victim feel remorse before dying. After the battle, Ken plants Smith's seed over his grave.

Ken learns that the prisoners that were transported with Rin were taken to a prison camp in a nearby valley. Ken manages to break the imprisoned villagers free, but during their escape they're all slaughtered in an ambush led by Mr. Heart, the last of the Four Jacks. While Heart's excess flesh proves resistant to his attacks, Ken eventually uses a techniques which penetrates through his body. From his battle with Heart, Ken learns an important clue which reveals to him the identity of King.

Having learned that King is none other than his old friend turned nemesis Shin, Ken remembers how a year ago Shin defeated him in combat, engraved the seven scars on his chest, and kidnapped his fiancee Yuria (Julia). Ken arrives at a local castle where Shin was staying, but only finds Shin's right-hand man Joker, who reveals that Shin and his gang has already left the castle, taking Yuria with him. Joker escapes and sets the castle ablaze with Ken inside, but Ken manages to escape, swearing to find Shin.

Ken and his friends arrive at an oasis under the surveillance of God's Army, a fanatical military group composed of former special forces members. Ken becomes a target for this group after Ken kills one of the security officers in battle.

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 penetrates the headquarters of God's Army and confronts their leader, the Colonel, a deluded follower of Shin who has mastered the art of Nanto Muonken.