This recap page contains unmarked spoilers, both for the game and possibly for the manga as well. Read on at your own risk.
Living in this post-apocalyptic wasteland is Kenshiro, successor of the martial art known as Hokuto Shinken. In the city of Southern Cross, Kenshiro confronts Shin, one of the masters of Nanto Seiken and a man whom Kenshiro once considered a friend, until he nearly killed him and kidnapped his fiancee Yuria.
On the topmost floor of a tower overlooking Southern Cross, Kenshiro approaches Shin. Shin reminds Kenshiro that the only reason he spared him was because Yuria begged him to in exchange for being his willing captive. He offers Kenshiro one last chance to leave with his life, but Kenshiro refuses: he has survived this long and clawed his way out of the depths of hell to take back Yuria and exact his revenge on Shin.
Once more, the two come to blows. This time, however, Kenshiro, driven by rage, overpowers Shin and hits him with a deadly attack. As he laid bleeding on the floor, Shin finally reveals that Yuria was gone, having thrown herself from the very tower on which they stood rather than continue to suffer under Shin's captivity, or watch as others suffered in his attempts to win her heart. He had everything a man could want; a city to rule over, and all the resources it contained...but it was all worthless without Yuria's love. As the effects of Kenshiro's attack take hold and he hemorrhages, Shin bids farewell to Kenshiro.
Afterwards, Kenshiro wanders the wastes, a broken man now that the love of his life was gone. He stumbles upon a village in an old automotive factory and sees raiders terrorizing the villagers to take their fuel. These lowly thugs are no match for Kenshiro, who dispatches them all with but a single touch. Unfortunately, the combination of exhaustion from wandering the wastes and despair over Yuria causes him to pass out.
Thankfully, a family he saved gives him shelter and water. He explains that he was in search of a woman named Yuria, which the young girl Ruka and her grandfather recognize, having seen a group of men escorting a beautiful woman by that very name pass through town. According to them, they were on their way to a place where people want for nothing; a place where fresh food, clean water, fuel, and even electricity are plentiful...a "city of miracles", just north of the factory town.
This is Kenshiro's best hope: even if it is but a rumor, he must pursue it. Before he leaves, he makes a promise with Ruka to bring her back what she most desires: all of the delicious apples she could ever want to eat.
Getting into the city proves to be a tall order, however: this city, named Eden, is bordered by a massive wall. Guards armed with crossbows stand like statues at the wall, stone-faced and deaf to the pleas of hundreds of wastelanders who also came pursuing the rumors of the city's bountiful resources. The only way in, Kenshiro learns, is with a special permit issued by the city's ruler, and there seems to be no way to get one...
Suddenly, raiders begin to attack innocent wastelanders, drawing Kenshiro's ire. These thugs are also powerless against Kenshiro's abilities.
As the dust settles, however, Kenshiro finds himself approached by a gunman. This armed soldier, Jagre, is the leader of Eden's Watch, and after seeing Kenshiro's fight, deems him an immutable danger to the public safety orders his immediate arrest and imprisonment. With the prison located within the city, it seems Kenshiro finally has his way in.
Breaking out of his cell proves a trifling matter, but evading the Watch may not be as easy. While evading detection, Kenshiro encounters a young woman with bright brown eyes and flowing blonde hair, who introduces herself as Xsana. Xsana deduces Kenshiro is an escaped convict, and when Kenshiro explains why he came to Eden, she suggests he enter tomorrow's Gladiator Games; a monthly tournament held in the city's Colosseum where prisoners fight for their freedom, and the champion can ask for any one wish from the city's ruler.
With freedom to pursue Yuria preferable to a life on the run, Kenshiro returns to his cell and awaits the break of dawn.
In the Colosseum, Eden's citizens, as well as Jagre, the Watch, and Eden's ruler gather to watch the Gladiator Games. Among the contestants fighting in the tournament are Eden's prisoners: thieves, rapists, murderers, and other scum of the earth, all of whom fall before Kenshiro.
Just as it seems that Kenshiro has claimed victory, however, he discovers that he has one final opponent to best: "Devil Rebirth", a massive mutant of a man standing ten times as tall as Kenshiro. To the crowd's surprise, Devil Rebirth is also toppled and knocked out. There can be no denying it: Kenshiro is the champion.
With that, the ruler of Eden approaches Kenshiro: a beautiful woman dressed in a white gown. When she removes her veil, Kenshiro recognizes her as Xsana.
"What can Eden grant a man of such power?" Xsana inquires.
"I need to search your city for a woman named Yuria..." Kenshiro answers, "...that is all I ask."
Thus, Xsana grants Kenshiro citizenship within Eden, and with it, the freedom he needs to find the love of his life.
There is little time to relax, however; the alarm is raised throughout the city as raiders are on the warpath towards Eden. These aren't just any raiders, however: they are the Army of Ruin, one of the largest raider groups in the wasteland, led by the mysterious masked warlord Kyo-Oh. The Army of Ruin had long been a problem for Eden as they had launched raids on the city for a long time, but this time, they have come prepared for a full-fledged invasion.
Two trucks in Kyo-Oh's convoy carrying gasoline tankers charge ahead and ram into Eden's wall, breaking it open and allowing raiders to flood into the city. Jagre goes to command the Watch and stop the raiders, and Kenshiro joins him. The two confront Kyo-Oh's lieutenant: Targa, a sadistic gunslinger who takes joy in gunning down innocents. Targa has Jagre at a disadvantage as he holds a hostage in front of Jagre, eventually executing him. Kenshiro intervenes and incapacitates Targa.
Before Targa can be taken in, however, Kyo-Oh jumps in and touches a pressure point on Jagre's neck, causing him to fall catatonic. He then takes Targa and retreats, along with his army...
There is still hope, however: a healer of peerless skill who can cure any illness and injury named Toki. Toki is a name Kenshiro is very familiar with: he was like a brother to Kenshiro and was one of the four disciples of Ryuken, the previous master of Hokuto Shinken, and was on the fast track to being named successor when the bombs fell. Toki risked his life to ensure Kenshiro and Yuria got to safety in a fallout shelter, but was exposed to nuclear fallout in the process. Afterwards, he became seriously ill from radiation poisoning and gave up his right to succession.
There was one problem, however: Toki was being imprisoned in Cassandra, a massive penal complex that none have ever left - at least, not alive. With time of the essence, Kenshiro prepares to disembark with Rihaku and Jagre. With help from Bat, a young boy whom Kenshiro befriended, he is able to get a working dune buggy which he uses to transport Jagre to Cassandra.
There, Kenshiro confronts Uighur, a massive man who acts as the warden of Cassandra. Uighur is under strict orders from Ken-Oh, a fearsome warlord, to prevent Kenshiro from rescuing Toki; but not even his size and strength avail him victory, as he falls to Kenshiro.
At long last, Kenshiro and Toki are reunited. Toki explains that Ken-Oh, who imprisoned him in Cassandra, is actually Raoh, their elder brother and another disciple of Hokuto Shinken. He was displeased with Kenshiro being named successor and began to gather a vast army as Ken-Oh in revenge, so that he could prove he was truly worthy. He was worried that if Kenshiro and Toki reunited, they would join forces against him. Since his escape would only draw Raoh to Eden and invite disaster, Toki decides to remain in Cassandra, but heals Jagre beforehand. Toki recognizes the attack used on Jagre as one belonging to a martial art known as Meito Kieiken; like Hokuto Shinken, Meito Kieiken uses pressure points to destroy the victim from the inside out, but instead of destroying the body, it destroys the mind.
Afterwards, Toki offers to spar with Kenshiro. When the two fight, it becomes clear that the brothers' philosophies to fighting are different: Toki's style of Hokuto Shinken favors defense and is likened to a still pond that moves with his opponent's attacks, while Kenshiro's take is based on all-out offense and is likened to a raging river. Toki advises Kenshiro that Raoh's fighting style is the same overwhelming force, and that if they fight as Kenshiro is now, Raoh would emerge victorious. He must continue to train himself, so that he can defeat Raoh when the time comes.
With night falling, Xsana invites Kenshiro outside to witness something incredible: water suddenly comes gushing out of pipes leading from Sphere City, and a building beneath the cathedral comes to life. It is a massive neon-lit nightclub, the crowning jewel of Eden. Xsana explains that every day, twice a day, water comes flowing out of Sphere City. The water that gushes out in the day is given to the citizens, while the water that comes at night powers the Nightclub and offers Eden's citizens a chance to enjoy themselves, even in the uncertain times following the Final War.
With that, Kenshiro makes his way to the Colosseum to undergo his trial. His accuser is Rei, a Nanto Seiken practitioner and master of one of the most powerful styles of Nanto martial arts: Nanto Suichoken.
As it turns out, Rihaku had led Rei here in search of his sister's abductor, hoping to arrange a fight between Rei and Kenshiro to test the mights of Hokuto Shinken and Nanto Seiken. In the end, Kenshiro emerges victorious. Rei is determined to keep fighting until he finds his sister, only for two of Rihaku's allies to come to the Colosseum with a woman in their care: a girl with flowing light-blue hair - Airi, Rei's beloved sister. Kenshiro's innocence is definitively proven as Rei and Airi tearfully reunite.
Afterwards, Xsana reveals the truth that Kenshiro had long sought: Yuria was, indeed, in Eden. She was last seen entering Sphere City to ascend to the top of the Tower of Miracles, which is said to possess miraculous healing properties. However, there was no way to enter Sphere City: after Yuria entered, the doors to Sphere City closed and have not reopened since. The last time it was opened was after her father, Nadai, took her mother in. When she entered the city to investigate, she witnessed Nadai kill his wife and her mother, and in retaliation, stabbed him.
The only way to see if Yuria was indeed in Sphere City is through the top of the glass dome encasing it, and the only place to peer inside is at the top of a mountain behind it. Unfortunately, the only way there is through the Cursed Village, so named because it was inhabited by those whose minds were lost to bloodlust and madness. So great is the Cursed Village's infamy that even Jagre is scared to go there, but go there Kenshiro and Jagre must.
Upon arriving in the foggy village, the two are beset by the villagers, violent and zombielike in their demeanor. Kenshiro soon recognizes that this isn't just any madness: it was the result of Meito Kieiken. Their minds long gone, Kenshiro can do naught but end the villagers' suffering.
Afterwards, as Jagre tends to the dead, Kenshiro makes his way to the cliff overlooking Sphere City. There, he finds himself confronted by a mysterious man wielding a strange martial art, whom Kenshiro realizes is Nadai. After the two fight, Kenshiro looks down the cliff and finally sees what he had long travelled, fought, and bled to see: Yuria! She was in a glass container at the top of the Tower of Miracles, which Nadai confirms had healing abilities. He explains that the doors of Sphere City would not open until Yuria had finally healed.
He knows about Sphere City because he had brought his wife there to use its healing properties to save her from a deadly illness. Doing so violated Eden's laws, but so determined was Nadai to save his love that he broke them gladly to save her. His wife, however, declared it was wrong to use the "sands" in Sphere City to save her and begged Nadai to end her life and spare her suffering. Nadai respected her wishes, right as Xsana stepped into the city. He survived the attempt on his life, but retreated from Eden, knowing Xsana would never understand what happened and never forgive him. He asks Kenshiro to keep his survival a secret, as well as to pass along some advice for Xsana: when the city's darkest hour comes, retreat to Eden's lowest levels.
However, dark times may soon be upon the city, for over the horizon, another army of raiders is approaching: not the Army of Ruin, but the Holy Imperial Army, led by the self-proclaimed Holy Emperor, Thouzer!
Within, he finds Thouzer holding Xsana captive. Kenshiro goes on the attack and launches an assault that strikes Thouzer's pressure points, ensuring his demise...or so he thinks: Thouzer declares himself completely immune to the effects of Hokuto Shinken, and the fact that he still stands, completely unaffected by Kenshiro's attack, seems to confirm as much. Even then, Kenshiro fights against Thouzer, determined to defeat him. As they fight, it soon dawns on Kenshiro why his attacks were ineffective: Thouzer was born with his heart and his other internal organs on the opposite side of his body, thus reversing his pressure points. With this knowledge, Kenshiro is finally able to turn the tide against Thouzer and emerge victorious.
With the Holy Emperor and successor of Nanto Houohken defeated, Xsana orders Thouzer to leave and take his soldiers with him: Eden will not fall this day. Thouzer reluctantly takes his leave, but not before leaving Kenshiro with a warning that he will return in due time.
Rei approaches Kenshiro during Xsana's speech and informs him of rumors about a man with seven scars causing trouble around Eden. Kenshiro is completely innocent, as Rei now realizes, and the two decide to work together to get to the bottom of this mystery. Asking around town, they learn that someone with seven scars had been causing trouble in various places of business, and appeared to be able to use Hokuto Shinken. This leaves little doubt to the true identity of the culprit: Jagi, another practitioner of Hokuto Shinken. Jagi was incensed over Kenshiro being named successor of Hokuto Shinken and lashed out at him, but was rebuffed and struck in the head with an attack that caused painful swelling. He now wore a helmet to conceal his disfigurement and keep the swelling under control, and had taken to exacting revenge by sullying Kenshiro's name.
Kenshiro and Rei's investigation reveals that Jagi had been kidnapping people with a similar height and build to himself. They find Jagi and his victims, only to see four people dressed in cloaks and face-concealing helmets. This, combined with Jagi exploiting his victim's pressure points to render them unable to speak, makes it nigh-impossible to determine who is the real Jagi. Kenshiro, however, is able to interrogate them by making them gesture "yes" and "no" to a series of questions. Exploiting his nature as a compulsive liar, Kenshiro determines who the real Jagi is.
With Jagi's victims freed, Kenshiro prepares to rectify his misguided attempt at granting his older brother mercy years ago, only for Jagi to reveal that he kidnapped Airi once more. Rei gives chase after Jagi, and Kenshiro follows him to the Colosseum.
In the Colosseum, Jagi reveals that he had teamed up with the Army of Ruin, with Targa nearby and Rei and Airi unconscious and held at spear-point, poised to kill them if Kenshiro moved while Jagi fought him. Kenshiro is able to defend himself ably, however, driving Jagi to demand Rei and Airi be killed. However, the Army of Ruin soldiers had been incapacitated by Meito Kieiken techniques. Kenshiro looks up in the stands and sees Nadai taking his leave, causing him to realize Nadai and Kyo-Oh are one and the same.
With Rei and Airi safe, Kenshiro is able to fight without restraint. In spite of his dirty tricks, Jagi loses to Kenshiro. During the fight, Rei regained consciousness, moved Airi to safety, then after Jagi is defeated by Kenshiro, attacks him with Nanto Seiken. His helmet cut to pieces, Jagi's head begins to swell. He begs Targa for help, but Targa leaves him to die as the effects of Rei's attack take hold and Jagi's body falls to pieces.
Jagre and the Watch apprehend Targa and the other Army of Ruin soldiers. Xsana approaches them and orders them to leave and inform Kyo-Oh that she wishes to seek peaceful cooperation with him.
Not long after, Raoh, the Ken-Oh, arrives with his army. To the surprise of Kenshiro and Jagre, Xsana kneels to Raoh and welcomes him to Eden. Together, they reveal that Eden had been built on Raoh's orders. As it turns out, Nadai was a loyal soldier of Ken-Oh's army, and together, they discovered the military base that would later be known as Sphere City, the two able to enter the city with Nadai's Meito Kieiken techniques, which can channel his life force as electricity to power the otherwise impenetrable doors. Upon discovering Sphere City's nuclear arsenal, Raoh declares that he has no need for such archaic weapons and instead leaves Sphere City under Nadai's protection, ordering him to build a city around it, use its reactor to provide for his people, and keep its dark secrets safe.
Upon the precipice overlooking Sphere City, Raoh sees Yuria in the recovery pod at the top of the Tower of Miracles, which he reveals is the control mechanism for Sphere City: when someone lays in the pod, hourglasses begin to drain away, indicating the time remaining until the nuclear arsenal is launched. Furthermore, Raoh reveals that Yuria is, in fact, the last living General of Nanto Seiken. To prevent a second nuclear apocalypse and assert his dominion over both Hokuto and Nanto, Raoh makes the decision to kill Yuria.
Kenshiro, however, will not have it. He challenges Raoh, and the two square off in the desert wastes. Raoh proves to be a powerful opponent, skilled in various techniques that would instantly kill most mortal men; but Kenshiro perseveres and emerges victorious. Raoh realizes the reason Kenshiro was chosen as successor: Ryuken, their teacher, said that the true power of Hokuto Shinken is born from love, and only one who knows sorrow can hope to master its ultimate technique. Kenshiro, whose love for Yuria knows no equal and whose strength was tempered by sorrow in his travels, is thus most fitting to be its successor. Raoh, nonetheless, will not see his ambitions end: he promises to destroy Hokuto and Nanto in time, and takes his leave for the time being.
Kenshiro learns that the best person to ask about the Army of Ruin's whereabouts is a "Sage of the Desert". When Kenshiro finds this man, who is an old acquaintance of Nadai, he learns that the Army of Ruin is nomadic, travelling across the wastes and stopping at Eden intermittently so Nadai can check on the city and the welfare of his daughter.
With help from Lyra, the Nightclub owner, Kenshiro is able to pin down the location of the Army of Ruin's camp, fighting his way through the soldiers therein and confronting Kyo-Oh. This "Kyo-Oh", however, is actually Targa in disguise, having donned the masquerade to distract Kenshiro so Nadai can slip into Eden!
When night falls, Nadai approaches the door into Sphere City and uses his Meito Kieiken techniques to open it. Xsana confronts him along with Kenshiro, who deduces that Nadai had come to kill Yuria and stop the nukes from launching. Kenshiro doesn't want the nukes to be unleashed, either, but is determined to save Yuria at all costs, bring him to blows with Nadai once more. In spite of Nadai using the most powerful techniques of Meito Kieiken, however, Kenshiro stops him.
Before Kenshiro can proceed into Sphere City, however, Targa appears, ordering the Army of Ruin to claim the City while Jagre and Lyra hold Xsana and Nadai hostage. It is revealed that Jagre is the son of Raja, the original leadeer of Eden's Watch, a man Nadai killed: not only to keep Sphere City's secrets safe, but in retaliation for shooting his wife, prompting him to try to save her three years ago. Lyra, too, is the child of those whom Nadai used his Meito Kieiken techniques on to safeguard Sphere City's secrets, in addition to countless others, all of whom Nadai felt guilty over. Jagre and Lyra teamed up with Targa, who was a soldier from the Final War who survived thanks to cybernetic implants, to carry out their revenge.
Jagre, however, begins to have second doubts and can't go through with killing Xsana when ordered by Targa, having fallen in love with her. Targa shoots Jagre, wounding him, before shooting Lyra dead. He isn't interested in revenge, however; what he wants is Sphere City itself. As Targa enters, Nadai tells Kenshiro that there may be a way to stop the nukes: an emergency shutoff switch at the top of the Tower of Miracles, which would close the dome and stop the nukes if launched...but doing so would mean giving up his own life. Kenshiro is fully prepared for death, however, if it means the chance to speak to Yuria just one last time.
Kenshiro gives chase after Targa, fighting his way through the Army of Ruin and confronting him at the top of the Tower of Miracles. Targe reveals that what he wants is to reign over a world that had been washed clean by nuclear hellfire as its new god, and to that end, he would take Yuria and make her bear his child. Kenshiro, unwilling to let this madman have his way, confronts Targa. In the end, in spite of his tricks and cybernetics, Kenshiro lands a fatal blow on Targa, killing him and ending his ambition.
The sand in the hourglasses run out, and the nuclear missiles begin to launch. Kenshiro finds the shutoff switch and presses it, closing the dome of Sphere City as Yuria finally awakens. The two embrace as the nukes begin to launch...
From all corners of the Wasteland, people watch as a light bright enough to make the sun cast a shadow radiates from Sphere City...
In the aftermath of this crisis, Eden still stands. Xsana continues to rule with benevolence over her people with Jagre at her side as Kenshiro and Yuria drive through the wastes, the two having survived thanks to Nadai, who pushed them into the Tower of Miracles's recovery pod to shield them from the explosions of the nuclear missiles. Yuria asks where Kenshiro plans to go. Kenshiro doesn't have an answer yet, beyond making a delivery of apples...