After stopping a fatal battle with Hajime Saito, a top government official asks Kenshin's help in killing a shadowy assassin who's threatening the future of the regime.
Following Kenshin's departure from the dojo, everyone, and especially Kaoru, are sad at being left behind. And while Saito tries to dissuade Sanosuke from following him, Megumi sends Kaoru to deliver some medicine that will aid in Kenshin's fight .
In the wake of Kenshin's departure, everyone at the dojo is anxious to join the battle against Shishio. With Sanosuke, Kaoru and Yahiko in pursuit, Kenshin encounters Misao, a young girl who also happens to be a clever thief.
Leaving Misao behind, Kenshin and Saito make their way inside Shishio's fortress. Following a confrontation with one of his most powerful henchmen, Kenshin is ready to take on Shishio himself.
As the showdown with Shishio approaches, Misao finds someone who could produce the sword Kenshin needs, only to be is disappointed when Shakkuu Arai refuses.
After watching an unarmed Kenshin bravely defend himself, Shakkuu Arai's only chance at saving his own son is to deliver his father's final reverse edge sword.
To prepare for Shishio, Kenshin asks a former teacher to help him master the last of his fighting techniques. However, Kenshin is distracted when Kaoru and Yahiko finally catch up with him after their long journey.
As Kenshin struggles to learn, Sijuro teaches him the most secret of his fighting techniques. And though Kenshin doesn't want to kill, it's inevitable if he is to beat Shishio. Meanwhile, Sanosuke is arrested during his search for Kenshin.
While waiting in jail, Sanosuke learns of Shishio's plan to overthrow the government by recruiting a deadly band of Samurai, including the blind warrior Usui, to defeat Kenshin and Saito.
Reunited with Sanosuke, Kenshin lays plans to stop Shishio from burning Tokyo to create the confusion he needs to overthrow the government. But Shishio harbors a surprise with his newest weapon, an ironclad battleship hidden inside another.
After Kenshin, Saito and Sanosuke destroy his battleship, Shishio issues his challenge for a final confrontation. And following Misao's defeat of the blind Samurai, Usui, Kenshin vows to spare the life of her mentor, Aoshi.
As Shishio prepares for battle, a henchmen suggests a plan to weaken Kenshin and his forces, ridding them of any opposition once and for all. As the moment of truth draws near, Sanosuke is pitted against Anji.
In his defeat of Usui, Saito exposes the blind warrior's plot to kill Shishio. And while Kaoru, Yahiko and Misao are preparing to defend themselves from an ambush, Kenshin readies for his fight against Aoshi.
Following his defeat by Kenshin, Aoshi vows to renounce Shishio. And while Shishio looks for clues to help in his impending fight with Kenshin, Kaoru, Yahiko and Misao fight to stay alive.
Despite the overwhelming odds, Kaoru, Yahiko and Misao continue to face warriors sent to eliminate them. But it's the arrival of Kenshin's teacher that turns the tide in their favor.
As Sanosuke looks on, Kenshin goes to battle with Souijuro, the emotionless assassin responsible for breaking his sword. Though Shishio is confident of the young warrior's ability, Kenshin may be able to win without having to resort to killing.
In an effort to explain Souijuro's emotionless posture, Kenshin recalls how the young assassin was rescued from a life of slavery and then taught to fight by Shishio.
In the face of Kenshin's probing questions, Souijuro's concentration is broken. In defeat, the young assassin returns his prized sword to Shishio, warning him of the danger that lays ahead.
As Kaoru and Yahiko anxiously await his return, a wounded but determined Kenshin arrives for his final showdown with Shishio, who is unwilling to have anyone stand in his way of controlling Japan's future.
In their long awaited battle, Kenshin and Shishio compare ideologies as well as fighting techniques. But once Shishio uses gunpowder to gain the upper hand, it looks like Kenshin is doomed.
As Aoshi tries to stop a takeover of the country, Kenshin poses Shishio with his greatest challenge. In his defeat of Usui, Saito exposes the blind warrior's plot to kill Shishio.
Kenshin's final effort to win the ultimate battle ends with Shishio destroying himself. But in the wake of Kenshin's victory, Shishio's closest aide vows revenge.
Following Shishio's defeat, his remaining allies put their fate in the hands of the government. While Kenshin is reunited with his Peace Force, the vanquished Shishio vows to take over Hell.
