Three major fires, one of which burns part of Edo Castle, since the New Year (1790) and an Iga ninja a mysterious suicide. Tonbei disappears then tries to kill Shintarō. Behind this is a ninja with formidable hypnotic skills and a contest of skills between ninja clans.

Lord Akizuki receives a ninja circular offering the services of Oki Senzō, a Kōshū ninja to help him achieve his ambition of supplanting Sadanobu. To demonstrate what a ninja is capable of, Akizuki is told to be at a temple at midnight where Sadanobu's most important man will be killed. As this is Shintarō things don't turn out that way and Senzō is killed.

Tonbei goes to fellow Iga ninja, Ippeita, to get him to take him and Shintarō to Togakure ninja, Gentatsu with whom Ippeita trained since the Togakure are the next in the contest. However, Ippeita and Gentatsu are the same man He tries to kill Shintarō after drugging Tonbei and fails.

Kongō finds Hakuun ninja, Naruko Ichiden who has given up being a ninja and buried the group's secret scroll in a false grave. He refuses to take part in the contest of skills but his daughter offers in his place, only asking that they be left in peace if she is successful. Of course Ichiden goes after her. Shintarō and Tonbei soon realise that the two are only doing this for each other and make Kongō believe they are dead so they can have a new life.

Two pickpockets who haunt a highway make a big mistake in their victims, three Noto ninja. One is killed and one of the Noto impersonates the other in order to lure Shintarō into a trap. When this fails the leader, disguised as a ferryman, tries to kill Shintarō.

Kirimaru, a young hot-headed Genmu ninja, takes up Kongō's challenge after testing his skills on the master ninja. He first lures Tonbei away, drugs him then disguises himself as an old priest in order to lure Shintarō into a shrine to kill him but Shintarō sees through the disguise and defeats him. Bested for the first time, Kirimaru bursts into tears then wants to come with them.

Kirimaru, now with Shintarō, discovers his sister Yuri has been captured by Kongō and he, Shintarō and Tonbei set out to rescue her. They overcome the guards at the temple where she is being held and Shintarō escapes with Yuri while Tonbei and Kirimaru fight off more ninja intending to join them later. Yuri persuades Shintarō to rest by a stream and then reveals herself to be a Ninkō ninja named Nagisa, seeking revenge on Shintarō for killing her father. She shoots him with a poison dart and he falls into the river.

Thanks to the help of a mysterious wandering monk who communicates with notes, Tonbei and Kirimaru find Shintarō who has been treated by the monk. Shintarō pretends to be dead, knowing that if Kongō thinks he's dead, he will release the real Yuri as he would have no further use for her. Nagisa and her band see Tonbei returning alone to Edo in tears and that is enough to convince them Shintarō is dead and they rush off to tell Kongō, who is somewhat sceptical and would like to see a head, at least, ta ever so. Kongō fetches Yuri from a cave and Kirimaru, who has followed Nagisa, decides to rescue her alone, against Shintarō's orders. Kongō taunts him and wounds him. Shintarō arrives with Tonbei and is set on by Nagisa and her band until the monk appears and reveals himself to be her father. Kongō, finding himself among friends but none of them his, vanishes.

Kongo uses a false message from Sadanobu to trick Shintarō into sending Tonbei back to Edo. On the way Kurozumi master ninja Dōjin captures him and uses him as bait to lure Shintarō to the Devil Mask House with all its traps. However, Fujibayashi Kaichi, an Iga ninja who accompanies him and who has fallen into a pit of spears is able to warn him in time so he doesn't suffer the same fate.

Shintarō realises that the Kurozumi ninja have a secret passage in and out of the house so uses that to return to try to rescue Tonbei. However, he finds himself trapped with Tonbei in a room with steel plates behind the walls and surrounded by fire. He is able to get the secret passage to work again and escapes. Dōjin and his men follow them to the small temple Shintarō had been using as a base and try to set fire to it. Kaichi and Tonbei kille the Kurozumi ninja while Dōjin - to his surprise - has the bow shot from his hands allowing Shintarō to kill him. Enter a new player, Gen-ryū Tarōbō who wants to kill Shintarō himself and substitutes his ninja school's name for that of the Muei-ryū on the challenge. He warns Shintarō and Tonbei not to take the Kiso-Kaidō Road but to take the Kōshū Road instead.

The Muei ninja have searched the Kiso-Kaidō road but can't find Shintarō. They wonder if he has taken another road. Tarōbō tries to persuade their boss, Urabe Hidari to sever his ties with Kongō. He refuses, they duel and Hidari is killed but not before he sends a top to Kongō with all that has happened. Tarōbō goes to the head of the next ninja in the challenge, the Shintō school but this turns out to be Kongō in disguise and he knows all that Tarōbō has done. In the ensuing duel, Kongō cuts off Tarōbō's arm. Meantime the Shintō ninja pour sleeping gas into Shintarō and Tonbei's room at the inn but they are waiting for them and kill them. On the road the next day Tarōbō intercepts them and warns them to be careful, there is danger ahead. He also swears revenge on Kongō. The next name on the challenge is Yūgasumi

Kongō creates a diversion to draw Tonbei away while he talks to Shintarō. He wants to warn him about Tarōbō who is not part of the challenge and over whom he has no control . He, too, wants to kill Shintarō but is not playing according to the rules. He says he will not let Tarōbō lay a finger on him. Shintarō. decides Kongō is a very strange man. He and Tonbei stop at an inn to dry off Tonbei's clothes and Tarōbō warns them ninja have infiltrated the inn. These are the Yūgasumi. Shintarō suggests they all leave the inn and fight outside so as not to endanger anyone. He kills them all out in the forest and follows a ninja who turns out to be Tarōbō. He tells him that the Yūgasumi betrayed Kongō and joined him. He tells Shintarō to throw down his swords but Kongō appears and tosses him one of his own. Tarōbō finds himself between the two armed men and disappears, swearing to do the same to Kongō. Kongō tells Shintarō he did not want him to die by Tarōbō's hands, that was all and not to get the wrong idea. He then walks away.

Kongo leaves a note in a boat instructing Shintarō and Tonbei to use it to cross the river (they are on the road to Odawara). Meantime Tarōbō persuades some of the other ninja to kill Kongō. They divert Shintarō and Tonbei and steal the boat. Tarōbō disguises himself as Shintarō in order to lure Kongō on to the boat where they ambush him. He is badly outnumbered but manages to hold his own until he is shot with a musket and falls into the water and disappears. He is found by the shore when Oboro who is a nun and Shūsaku who is staying at the convent are out gathering flowers. They take him back to the convent where he is treated by a doctor but the other ninja have arrived and demand he be handed over. Oboro and Koshinjo (the abbess) refuse. Shūsaku manages to get word to Shintarō so when the ninja break into Kongō’s room the figure in the bed turns out to be Shintarō. Shintarō despatches the ninja but then is confronted by a very weak Kongō who challenges him to a duel. Kongō collapses before it really starts. The next morning Tonbei awakes in the convent to the nuns’ sutra-chanting to find a note from Shintarō saying he was embarking on a journey and did not know if he would ever return or what where he was going Tonbei, Shūsaku , Koshinjo and Oboro run down to the shore and see Shintarō standing in a boat being rowed by Kongō, heading out to sea.