Sadanobu summons some close associates to tell them of his mission to Kyoto, ostensibly to oversee the rebuilding of the Imperial palace destroyed in a fire some months before but actually to root out a conspiracy against the shogunate as Lord Owari has offered to rebuilt the palace at his own expense, thus curry favour with the emperor. Plus there are documents which reveal just how vulnerable the shogunate is. High Priest Donkai asks Shintarō to defend Sadanobu on his journey but Shintarō refuses, having renounced the sword and gone fishing because of all the killing he had to do with the Kōga ninja and Takeda Shingen's treasure.

At Totsuka, the 6th station of the 53 on the Tokaido, Momochi Genkurō and his 10 master ninja, from the Manji Valley, who have been hired by Lord Owari to assassinate Sadanobu, plan to attack his caravan with a rocket packed with gunpowder, and fired by their best archer Koheita.

At Fujisawa, the 7th station, Gensai, one of the Iga group, bribes a maid at the inn Sadanobu is staying at, to put sleeping powder in the well. She immediately repents of her action and is saved by Shintarō, who cuts off Gensai's arm in a duel.

Discontented with Tonbei's leadership, Sanosuke is forced into working for Genkurō, to lure Shintarō into a trap with a false message from Sadanobu who is staying at Odawara Castle, Odawara being the 10th station.

Okayo, the ninja sister of Koheita, the archer, assumes the guise of an innocent traveller who has had her papers stolen but needs to get through the checkpoint at Hakone, the 11th station to visit her sick mother. Shintarō helps her but Tonbei and Sanosuke, who is trying to redeem himself are suspicious.

At Yoshiwara, the 15th station, Genkurō challenges Shintarō to a duel. Okayo is his guide, so she can watch him be destroyed. The plan is that Tonbei's Iga ninja will also follow Shintarō to see if they can help leaving Sadanobu unguarded. Both Shintarō and Genkurō are wounded but Genkurō's sword had poison on it. However, Okayo gives Shintarō the antidote.

Ninja Toma the Face-stealer impersonates Tonbei and lures Shintarō to the Utsunoya Pass, near the 22nd station, and pushes him over a cliff, then goes back to Fuchū, the 20th station (now Shizuoka City), to eliminate Sadanobu's ninja guard. Meantime, the real Tonbei is captive in a hut watched over by Okayo, who is torn by appeals to her humanity by remembrances of Shintaro and by Tonbei's pleas to free him so he can try to save Sadanobu. She draws a knife to free him and says she will pray for the souls of Shintarō and Koheita just as Toma returns who kills her as a traitor.

The Tokaido divides at Kakegawa, the 27th station, into two parallel roads. Genkurō is not sure which one Sadanobu will take but becomes suspicious when a box of pilgrims' clothes is found at the inn Sadanobu's party is staying at. Gensai suggests they attack both roads. They think they have found Sadanobu disguised as a komusō (itinerant flute-playing priest), having found a group of pilgrims to be what just that. But all is not what it seems.

At Miya, the 42nd station, Sadanobu is to take ship to reach his next destination, Kuwana, the 43rd station. Genkurō cannot attack him where he is as they are in Lord Owari's territory. However, he plans to load gunpowder into Sadanobu's boat to destroy him on the sea.

Genkuro and his remaining ninja go to Onime Dōgan, an ancient master ninja who has 4 pupils, to ask his help, as do Shintarō and Tonbei. Dōgan refuses both groups, not wanting to become involved.

Suiki, one of Dōgan's pupils is persuaded to join Genkurō. Genkurō kills him and uses a stolen case to incriminate Shintarō. Suiki was actually Dōgan's only grandson and the old man swears vengeance. When he discovers the truth, he sends the remaining three pupils with Shintarō. Sadanobu is at nearby Kameyama, the 47th station.

At Minakuchi, the 51st station, 40 miles from Kyoto and Gensai's home town, Genkurō's group is joined by Wolf Ninja who fight as a pack. Gensai uses his local knowledge to infiltrate the castle where Sadanobu is staying and put sleeping powder in the well. However, his thirst for revenge against Shintarō for cutting off his arm gets the better of him and he hunts him down instead of returning to Genkurō. He is apparently killed.

Otsu, just 10 miles from Kyoto, is Genkurō's last chance to kill Sadanobu.. The councillor is persuaded to hide in the inn's warehouse while Shintarō takes his place in his room. However, Genkurō is aware of the trick and captures Sadanobu and takes him to a boat, rows him off shore and offers him a choice of being killed or committing suicide. However, the other ninja in the boat turns out to be Shintarō who attacks Genkurō, they duel and Genkurō, mortally wounded by Shintarō's sword thrown into his back, kills himself. Sadanobu reaches Kyoto in safety and Tonbei offers to pray for those of his Iga gorup who were killed and Shintarō suggests they also pray for Genkurō and his group.

New adventure series set in medieval Japan telling of Shintaro the master swordsman and of his relentless search for his enemies, the black robed society known as the Koga ninja. On a Tokyo street at midnight, a lonely traveller is passing when a dark figure springs out of the darkness, kills him and begins ransacking his pockets in a hasty search for a bag of gold he was taking to one of the Shogun's ministers.

The first of the 13 ninja of the Koga society is dead after challenging Shintaro to a fight. Now Shintaro and his young companion,. Shusaku, are in search of another challenger.

While walking along a dusty road on their way to Kofu, Shintaro and Shusaku notice an express courier in a great hurry and they catch sight of a ninja knife falling out of his pocket. That night Shusaku is kidnapped.

While he and his companions are resting in an inn, Shintaro sees a scared rat running from the closet and realises there is someone hiding inside.

When the leader of the infamous Koga society harangues Kurobei for failing to rescue another ninja from Shintaro, Kurobei decides to turn against the society and join the master swordsman.

After sneaking out of a temple in which Shintaro has sought refuge for the night, Kurobei is challenged by a black clad figure in the belfry.

Shintaro goes to the rescue when he sees a band of villainous sedan-chair carriers running off with a girl named Chikage. Then he decides to help her locate her father.

Shintaro and his young companion have finally arrived in Kofu after many adventures but their arrival is being observed from afar by Sarobei and Genzo, two more master ninja.

The Koga ninja has been committing a series of crimes including arson and murder with the sole purpose of coaxing Shintaro into the open so he can be their next victim.

Ninja Kogento enables an expert rifleman to do away with Shintaro.

Shintaro offers to escort some fugitives from the Koga ninja into Kofu though this means he will have to walk back towards his enemies who are pursuing him.

While searching for a secret entrance to a hidden gold mine, Shintaro sees a group of ninja attacking a woodsman.

Shintaro and Shusaku, while journeying through the mountains, save the life of a farmer who is hanging upside down in a tree. He tells them he was attacked by the Koga and Shintaro realises they are nearby.

Shintarō saves a young Ainu wrongly accused of murder, relying on his wits and his pistol.

Shintarō captures an escaped thief and takes him to the town of Kiritap to be held until Kiba arrives. However, the villagers' greed allows the thief to free himself and kill one of them and hold another to ransom.

Shintarō comes upon a woman and her young son who are being terrorised by a loan-shark and his offsider, a disreputable but skilled swordsman.

A group of Ainu take a wagon carrying gold from the goldmine on the Shibuchari River in revenge for the death of the son of one of them caused by two of the guards.

A shipwrecked rōnin impersonates Matsudaira Nobuchiyo at the instigation of a smuggler of guns so he can get them to the Ainu who has purchased them.

Shintarō helps a young boy find his mother who was taken by Onibishi, an Ainu chief. Kiba persuades Onibishi to set a trap for Shintarō.

Shintarō, Sanpei and the refugee Ainu women continue on their way to Kunashiri Island. Sanpei mistakenly thinks Shintarō is really after Ainu treasure. Kiba and Onibisho are following them and try to ambush them at Hell Valley.

Goromatsu's two outlaw brothers break him out of Shiranuka Gaol where he is awaiting transfer to Matsumae. He vows to kill Kiba and enlists their help.

Shintarō encounters Tendō Sawanosuke, a blind rōnin and his young daughter who are being harassed by Hidaya's bullies. Sawanosuke is well able to defeat them and Hidaya hires him to kill Shintarō because he has a deed of his. He wants to get Shintarō before Kiba does.

Habaro a young part-Japanese Ainu hunter is persuaded by an ambitious gang leader to kill his boss so he can take over but is shot in turn. Shintarō is accused of the murders but has help from an old friend, a geisha he knew in Edo.

Shintarō helps a brother and sister from Aizu take revenge on the man who killed their father who is now using another name and is the sword instructor for the Matsumae Clan. Kiba plays something of a double game.

Chusuke the Weasel returns to Usu seeking Yaichi, the man who put him in gaol. None of the villagers will stand by Yaichi. They think he should leave town and then maybe Chusuke won't bother them. Yaichi's son worships him and Yaichi fears to disappoint him because deep down he is afraid.

Matsumae government convoys and samurai have been attacked by a man in white who claims to the onmitsu. Shintarō resolves to unmask the impostor and clear his own name. He calls on Kiba to witness this. Kiba does so but still wants him dead to fulfil his mission.