Years has passed since Kenshiro disappeared following his final battle with Raoh and in the years since he's been gone, the Army of the Celestial Emperor has began to expand their territory through threat and oppression. Bat and Lin, Kenshiro's former companions, are now grown up and are leading a resistance movement known as the North Star Army.

A mysterious drifter wanders into a town where the remnants of the Red Dragon Party, a resistance movement that once opposed the Celestial Emperor's army in the past.

After being reunited with Bat and Lin, Kenshiro decides to join their cause, giving the North Star Army a needed boost in morale. A bounty is placed on Kenshiro's head and a man named Ein decides to take the offer.

As the North Star Army begins to liberate another one of the Celestial Emperor's areas, Kenshiro is forced to return to Mamiya's village to confront Solia of the Purple Light, a master of Gento Kōken who has been ordered to annihilate anyone associated with the Hokuto and Nanto schools.

While attempting to catch up with Bat and Lin, Kenshiro is confronted by Shoki of the Red Light, a man who once helped Kenshiro in the past, while Bat and Lin lead a desperate battle against the Golden General Falco, the strongest of the Gento warriors.

Just when Falco is about to execute Lin in front of her supporters, Falco is challenged to combat by the Harn Brothers, Haz and Gil, who are seeking revenge against Falco for killing most of the Nanto Seiken masters, while Ein tries to lure Kenshiro to his traps.

After Ein decides to switch sides and join the North Star Army, his former recruiter Beron decides to take revenge by kidnapping his "little lady", Asuka.

As Kenshiro and the North Star Army approaches the Imperial Capital, Shoki of the Red Light decides to revolt against the Viceroy Jakoh, who is holding the Celestial Emperor hostage and forcing Falco to do his evil bidding.

Kenshiro confronts the renegade Gento warrior Boltz of the Blue Light, while Falco hands out a detonator to his lover Myu, which is triggered to destroy the foundation of the Imperial Capital, in case he loses to Kenshiro.

Lin enters the Imperial Capital along with Bat and Lin, sensing that the Celestial Emperor is calling out for her, while Kenshiro and Falco begins their battle.

Jako triggers bombs that collapse the ceiling of the cave in order to kill Lynn and Luise, but Ain shields with his body and protects the two sisters; weakened by the impact he still manages with his fists to open a gap and bring the prisoners to safety, but bleeding from the effort.

Lin and her group manage to escape from Jakoh's underground dungeon, but at the expense of Ein's life. With the Celestial Empress Lui now free, Jakoh loses his hold on Falco and begins to flee for his life.