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.

Bato spots Rin in a truck full of captured villagers being taken to the village of Dorado, which is occupied by the King gang. On their way there, Ken encounters two of remaining Jacks, Diamond and Club, who are torturing the villagers of Dorado. With Bato's help, Ken is reunited with Rin.

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.

Ken and his friends visit a village where young men and women are offered as slaves to Madam Patra, a local sorceress who controls the village's water supply.

Ken and his companions meet Taki, an old friend of Bato. Taki takes them to his home village where Auntie Toyo, an elderly woman who takes care of orphaned and abandoned children, is trying to dig a well. Unaware to him, the Warriors biker gang led by Jackal have followed Ken, seeking to claim Toyo's village as their new hideout.

After Toyo is killed by Jackal, Ken leaves Bato and Rin to watch over Toyo's orphans while he chases after Jackal's gang. While searching for clues to Jackal's destination, Ken encounters Fox, Jackal's right-hand man.

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.

Ken and his friends visit a village where their local doctor, a man named Duran, offers his hospitality. However, Duran's former partner-in-crime, Dante, is hired by Shin to hunt down Ken. Dante takes the opportunity of the situation to blackmail Duran to do his bidding.

Ken and his friend must save a haunted village from Zaria, a witchdoctor who uses a strange hypnosis technique that turns villagers into mind-controlled slaves.

Ken is caught at the middle of a gang war between the Scorpions and the Snakes, each seeking to recruit Ken to their side.

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.

One of King's subordinate gangs attacks a village Ken is visiting, while Yuria attempts to escape from Southern Cross with the help of her young maid Saki.

Ken is forced to return to Jeena village when Garekki of the Gold Wolf gang attempts to invade it, while Saki's elder brother, Temjina, escapes from Southern Cross, seeking to tell Ken of Yuria's whereabouts.

With Ken having learned the location of the city of Southern Cross from Temjina's dying words, Shin deploys a giant gunship as his last resource.

With Ken presumed dead, General Barcom leads a mutiny against Shin, seeking to take over the King gang for himself. Elsewhere, Joker searches the wreckage of the gunship for Ken's body, unconvinced that he is actually dead.

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.