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.