In Indonesia, four years after the purge of the Qing Ban, Dutch soldiers intimidate locals while looking for Yan Wang and Erika. Kenshiro disposes of them but exposes his location, while Yasaka visits Erika in an orphanage, observed by Dutch troops. Meanwhile, officer Van Der Kolk carries out murderous clinical trials to create ultimate soldiers at a Dutch outpost. In their secret headquarters, supporters of Migado Migadol, including Van Der Kolk, listen to Simeon announce his plan to re-create the world according to their prophesy. Back in town, the woman claiming to be the sister of Liu Fei Yan challenges Kenshiro.

Liu Fei Yan’s sister, Fei He, attacks Kenshiro as she believes he killed Liu Fei Yan, but he does not fight back. She explains that 8 years ago, as an orphaned petty thief, she encountered Liu Fei Yan and eventually traveled with him for 4 years as his apprentice. When she reached Shanghai, she was told by Tian Xue-Fang that Kenshiro had killed her adopted "brother". Meanwhile, a group of Van Der Kolk's superhuman ultimate soldiers attack the orphanage to abduct Erika, but are delayed by Yasaka until Kenshiro and a Yu Ling arrive. Together they defeat the ultimate soldiers and Kenshiro releases them from their internal torment to grant them a peaceful death. Yu Ling and Liu Fei He escape with Erika and the other children just as Van Der Kolk arrives and prepares to attack Kenshiro.

Kolk thinks he has immobilized Kenshiro, but painfully realizes that has not. In an effort to defeat Kenshiro, Kolk injects his own serum into himself to increase his strength and speed, but to no avail. Kenshiro immobilizes him and Kolk reveals that he is a descendant of the Nahash people, planning to recreate the world with Migadol's Thunderbolts and Erika's memories are the key. Meanwhile, Simeon approaches the hideout of Liu Fei He, Erika and the other children but is initially stopped by Yasaka. However Simeon's superior power overwhelms Yasaka, and he abducts Erika and the unconscious Yasaka. Back at their secret headquarters, the Nahash revere Erika as Migadol in accordance with their prophesy which states that the chosen child will receive Migadol's thunderbolts from the heavens.

Pan Yu Ling tells Fei He that Yasaka killed Liu Fei Yan, but that his dying words were to not seek revenge, however she has trouble reconciling this information. Meanwhile the Nahash priests try to extract information about Migadol's thunderbolts from Erika, a nuclear fission device designed by her father. A flashback shows how Erika's father made her promise to keep the information secret before he died and Fei Yan took Erika to safety. Tian Xue-Fang and Hippo offer to help Pan Yu Ling against their common enemy, the Nahash and she accepts. Fei He intercepts them as they leave, asserting that they plan to double-cross Pan Yu Ling, so she blackmails them into helping her find Yasaka. Meanwhile Yasaka realizes that Erika is being kept prisoner in the same building.

Kenshiro trades insults with Simeon and then engages him in battle. Meanwhile Himuka takes Erika and extracts from her the location of the Nahash jewels which are in Japan. Meanwhile the battle between Kenshiro and Simeon continues, with Simeon surprised at Kenshiro's resistance and assertion that the Heaven Dipper Sacred Yin Fist is stale and has not progressed like the continually evolving Divine Fist of the North Star. Eventually Kenshiro prevails, shattering Simeon's dreams for fulfillment of the Nahash prophesy. Elsewhere within the complex, Himuka savagely beats Yasaka who refuses to give up, then Fei He arrives to challenge Himuka, but Yasaka intervenes and takes a punishing blow.

Tian Xue-Fang and Hippo find their way into the control room of the Nahash headquarters, and Tain accidentally presses a self destruct button. Before Himuka can kill Yasaka, an explosion rips through the building. Yasaka saves Erika and Fei He and asks her to look after Erika, before he dies, buried under rubble. Himuka finds the injured Simeon and accuses him of naivety and declares that he plans to use the Migadol's thunderbolts himself. Incredulous, Simeon recalls how years ago Simeon swore fealty to him and together they studied the four pillars of the Heaven Dipper: stealing, accumulating, rebinding and unbinding. Confronted by Himuka's ambition and betrayal, Simeon destroys himself as punishment for being deceived.

Himuka visits Ramon and demands the two jewels that Yasaka gave to him four years ago. Ramon's father Tenshin reveals that Himuka's real identity is Kasumi Kenshin, Ramon's adopted brother. Tenshin taught Kenshin Hokuto Shinken even though he thought his temperament was unsuitable. Then one day, their housekeeper Marie, whom Kenshin secretly loved, was killed in a bombardment and he retaliated with extreme force. He then wandered the world and learned the Heaven Dipper Sacred Yin Fist, but while being hunted by the Nahash for betraying them, he fell from a cliff. Tenshin recovered Kenshin, but he sealed away his memories using pressure points. Now Tenshin again tries to seal away his former pupil's strength, but Himuka is too powerful and kills Tenshin, his former master.

Following Yasaka's funeral, Erika is diagnosed with potential brain damage, meanwhile she asks Fei He to tell her about Fei Yan. Later, Ramon arrives with the two jewels and gives them to Kenshiro and Yu Lig for safekeeping. In a flashback, Kenshiro recalls his time years earlier training with Kenshin and the threat he posed then, and possibly in the future. Suddenly Kenshin launches an attack demanding Erika, but Kenshiro comes out to face him in what may be the battle for his life.

Kenshiro and Kenshin fundamentally disagree about the future of humanity, with Kenshin believing that a complete re-genesis is required. Kenshiro then has to defend himself against Kenshin's powerful combined techniques attacks of Hokuto Shinken and Tento Seiin Ken. To save Kenshiro, Erika offers Kenshin the jewels, and she leaves with him, but not before he strikes Kenshiro's Shinkensutsu pressure point which will cause him to die within three days. Kenshiro asks Romon to strike his Shinreidai pressure point to prolong his life but at the cost of extreme agony. Meanwhile, Fei Yan proposes that they all go to Nohal Naha in an attempt to stop Kenshin. Romon declares his love for Fei He, but she doesn’t hear him, intent on following the way of Hokuto Shinken. Fei Yan spends their last night together with Kenshiro.

Erika accuses Kenshin of exploiting the Nahash and their prophesy for his own gain and she attempts to destroy herself and the temple but is easily thwarted by Kenshin. Kenshin then strikes a pressure point on her head to force her to reveal her father’s plans for the nuclear fission device. Suddenly Kenshiro, Ramon and Fei Yan arrive and stop the process. Kenshiro uses the Nil-Thought Rebirth technique to strike Kenshin thereby avoiding avoid his counterattacks while Ramon and Fei Yan escape with Erika whose memory has been erased. With Erika removed, Kenshiro again engages Kenshin in battle.

Kenshin attacks Kenshiro with a barrage of punishing blows, then evokes Black Cave Heavenly Death which envelops Kenshiro in darkness. However even within the darkness, Kenshiro's pengyou, Charles de Guise, Liu Fei Yan and Yasaka light the way for him and he finds his way back to Kenshin. Kenshiro utilizes the ultimate technique of Blue Dragon Heavenly Silk as he and Kenshin battle each other with their fists until Kenshiro lands a punishing blow on Kenshin's chest. They admit their grudging respect for each other and dedication to achieving their ideals, but Kenshin tricks Kenshiro into delivering a killing blow finally ending his dream for a re-genesis. Later, Fei Yan returns to the orphanage with Fei He and Erika, and Ramon continues his training. Elsewhere, Kenshiro lays down on a rocky outcrop above the clouds, gazing at the blue sky as he smokes his last cigarette.