A masked ninja called Yami Hōshi (lit. Black Priest) has been killing rice merchants in Edo much to the glee of the local populace as these merchants were widely believed to have been involved in the black market rice trade. This bandit leaves behind notes taunting the authorities that he has stolen the merchants’ gold to return it to whom it belongs. There is much unrest as all Edo is talking about the thefts and murders, the authorities look like fools and there is a rumour that the previous chief minister, Tanuma Okitsugu was poisoned (suggesting this story is set in 1788 as indeed there were riots and belief that merchants were profiteering from the famine). In the meantime a young samurai spy, Ōtsuki Gorōta, has been sent to Owari (curiously called Ohari in the English dub of this story) and has been missing a year. The shogun is concerned that the murders are politically motivated and Matsudaira Sadanobu, the new chief minister, summons Tonbei for a report. Shintarō is returning from Hakone and is attacked by a deranged Gorōta. Once Gorōta realises that Shintarō is also a spy samurai he manages to warn him about 13 Black ninja and the ‘Owari secret", then dies. Shintarō kills one of them, Yumesuke the Weasel, unaware he and Tonbei have been followed by Gensai in disguise as an old man. Shūsaku comes to Edo to find Shintarō as instructed by his dying father so he can be brought up as a samurai.

The Black Ninja have started systematically killing spy samurai in place on the staff of various domain lords, and identifying them as such. This is so the domain lords will become angry that the shogunate so distrusts them that it is spying on them. The Black Ninja intend to take advantage of the dissatisfaction of the clans. Sanzō the Swift, disguised as a blind masseur, passes a fake message from Kanabe Sakunosuke, the spy in the Itō clan to Kijima the spy in the Hotta clan to draw the latter out in order to kill him. However, Shintarō substitutes for Kijima at the rendezvous, Shiba Temple. Sanzō is badly wounded, swallows a suicide pill and explodes.

Shūsaku reveals the circumstances which have brought him to Edo (we learn he is 8 years old). Shintarō takes him to Keiko, Gorōta’s sister, for safe-keeping. The Black Ninja poison the well intending to kill Shintarō. One of the Black Ninja, Mosuke the Tiger, is caught by the police and secured in Denmacho Gaol from which no one has escaped. His companion, Gondayū the Shooting Star, and Gensai break him out but at the temple which is the Black Ninja’s hideout, Gondayū is suspicious that Mosuke would have been caught in the first place as he is too good. Sure enough, "Mosuke" turns out to be Tonbei in disguise. Gondayū uses a disappearing trick to escape and attack Shintarō who is coming to the temple. They fight and Gondayū is killed and Tonbei, who is tied to a tree outside is rescued.

Hakuunsai, head of the Owari ninja, arrives at the Sakai residence, disguised as an itinerant priest. He brings a message from the Lord of Owari encouraging all the domain lords to sign an agreement to unite against the shogunate. This conversation is overheard by the spy samurai Kazama who uses a listening device which Hakuunsai spots and uses to bolster his case, that it is a fine reward for loyalty to be spied on by the shogunate. He says he will take care of the matter and kills Kazama and also his associate, Nakata Nobuhiko. Meantime Tonbei furthers Shūsaku’s ninja education by telling him about (and how to make) ninja ‘miracle pills’ designed to sustain them while on a mission. Shūsaku wants to help find Kazama and cites how he helped Tonbei get to Kōfu (continuity blunder here – Tonbei didn’t join Shintarō until the following story). Tonbei tricks him and runs out to follow a mysterious chest being taken from the Sakai residence to the Dark Temple (where Gondayū was killed). Tombei is captured in the temple. Shintarō enters, opens the chest and is attacked by the ninja inside. Shūsaku rescues Tonbei who comes to Shintarō’s aid. He captures a ninja who bites his tongue and dies rather than reveal any information. Shintarō tells Shūsaku not to look and doesn’t look himself.

Gensai reports to Hakuunsai that there are now no more spy samurai in Edo. Gensai is doubtful when he is told that the Black Ninja will leave Edo when their lord does as he swears on his sword he wants to kill Shintarō himself because of all the ninja he has killed. Shintarō and Tonbei decide to capture a Black Ninja to extract information from him. Yūzō and two other ninja attempt to assassinate Shintarō but are tricked by Tonbei. He captures one who is killed by Gensai, and impersonates another. Gensai realises they have a spy in their midst and Tonbei is captured. Shintarō sends Shūsaku to safety and goes after Tonbei and fights with Gensai. Shūsaku follows. Gensai threatens Tonbei with his sword, forcing Shintarō to drop his sword. He then taunts Shintarō with cutting off his ears, nose, etc. while Shūsaku retrieves the sword and cuts Tonbei loose. Gensai retreats. Tonbei, Shintarō and Shūsaku set off for Oshi Castle in Musashi Province, home of the Abe clan, some 200 miles away.

Tadaoka, a retainer, is the key to persuading the Abe clan to join the Black Ninja compact to replace the shogun with the Lord of Owari. Hakuunsai approaches him. Tadaoka refuses and threatens to report Hakuunsai to the shogunate. Hakuunsai counters with incriminating though false letters in a box found mysteriously in Tadaoka’s rooms. He threatens to ruin him unless he signs. Chiyo, the daughter of Hiyama, the spy samurai assigned to the Abe clan and herself a ninja, overhears this and is attacked by Gensai {"Women die, too" says this paragon of chivalry) but Tonbei intervenes. She reports to Hiyama and says that the box of letters must not be taken to Edo because, although it will also incriminate the Owari, their name will disappear leaving just the Abe clan’s. He agrees. Shintarō retrieves the box of letters. Chiyo and Kiyama agree not to spy on the Abe any more. Shintarō fights Gensai and Hakuunsai but Hakuunsai runs off into a procession with the shogun’s crest on it. (During this, Tonbei gives Shūsaku more ninja information, this time on disguises, weapons and medicine.)

Jinpachi , a Kōga puppet ninja, reports to Gensai as their master, the Retired Lord of Owari, passes in his palanquin. Shintarō recognises Jinpachi and Tonbei follows him. Jinpachi challenges him to a duel of ninja skills. Shintarō and Shūsaku find Hakuunsai by a stream and follow him. Jinpachi tricks Tonbei and catches up with Shintarō and Shūsaku and challenges the former. Hakuunsai and his men also attack but Shintarō defeats them. He takes Shūsaku, who was wounded in the foot in the fight, to a temple but the temple is surrounded by Black Ninja. Tonbei arrives and takes Shūsaku to safety while Shintarō fights. Jinpachi is killed.

Gensai reports to the Retired Lord of Owari. Shintarō, Tonbei and Shūsaku are in the inn across the road. Tonbei teaches Shūsaku a technique to calm oneself, then apologises for teaching ninja skills. Shintarō replies, "I may fight against ninja but I don’t hate them. The ninja spirit has goodness in it." Nishina, a samurai with the convoy taking gold to Edo reports to Captain Shindo he has seen signal flares and fears the gold may be stolen. Shindo, who is a lazy drunkard, simply orders more sake for the men. The Retired Lord lures Shintarō away so Gensai and his men can steal the gold. However, Nishina investigates the flares, and encounters Tonbei who shows him his ID and explains about the Black Ninja. Shindo still won’t listen. Kakuzō the Hawk, disguised as a bearer in the convoy lures Nishina away while the robbery takes place. Shintarō and Tonbei hide in the storehouse where the gold is and dispatch the thieves. Shintarō kills Kakuzō. Prior to this Gensai has fled on horseback, almost running Tonbei down.

Nuinosuke and his sister, Ritsu, the children of a man ordered to kill himself in Owari, want revenge and attack the Retired Lord and his train. Shintarō and Tonbei rescue the pair. They find themselves in agreement with Shintarō that the Retired Lord has to go to save the Owari clan. Tonbei has his doubts about the siblings and suspects Hakuunsai sent them to confuse them but Shintarō has faith in them. While at the inn, Shinshūya, Shintarō and Shūsaku are attacked by a pair of Black Ninja and Ritsu’s brother is also wounded. Tonbei and Ritsu go to Owari to gather like minded people but Ritsu reveals herself to be a Black Ninja named Kazeba and attacks Tonbei. Meantime Shintarō, Shūsaku and Nuinosuke follow the Retired Lord until Nuinosuke reveals himself to be a Black Ninja known as Flying Eagle and attacks Shintarō in a temple. They fight and Flying Eagle is killed. Kazeba swears revenge on her brother’s killer.

Shintaro, Tonbei and Shusaku have now reached Lake Suwa, 100 miles southwest of Edo in Shinano province, and relax in a bath. Gensai reports to the Retired Lord at an inn that the agreement has now been signed and Hakuunsai will bring it in a few days. He goes to the wood where Kazeba has been captured. He rebukes her for not wanting revenge for her brother, saying that she was born a ninja, and remains one until she dies so she is a traitor. "I am going to show you ninja justice" and then beats seven bells out of her with his sheathed sword as she hangs bound round the arms from a branch (Gensai had a tendency to quote the "Book of Ninja"). Tonbei witnesses this and reports it to Shintarō who rescues her despite Tonbei’s misgivings this could be a trap. Kazeba offers to lead them to the temple where the agreement is to be handed over. Again Tonbei is suspicious but they go anyway and it is a trap. Shintarō fights Hakuunsai while Tonbei takes on Gensai, then Kazeba throws a ring of fire around Shintarō, "For my brother!" In the struggle, Kazeba catches fire. Shintarō gets the agreement and saves Kazeba but the document is false and merely states, "We have gone to Owari."

There are three checkpoints on the way from Shinano province to Owari province. One of them Ogase, was where Gorōta was discovered as a spy. Shintarō decides it would be better to go around over the mountains and avoid the checkpoints but they need a guide. Tonbei goes in disguise to Ogase to contact Seihachi, the spy samurai there who owns a small medicine shop. At the checkpoint, Gensai is sitting with the guards, giving the nod or not to those passing through. Tonbei passes through safely despite Gensai giving him a hard stare and reaches Seihachi, unaware that the identity of the spy samurai is known to the Black Ninja as it had been discovered by Ghost Koroku of Koga. Seihachi says the hunter, Sakuzō who lives on Eagle Mountain will guide them. Kazeba comes to warn them and offers to show them another way but she is not believed. Shintarō will go over the mountain while Tonbei goes through the checkpoint. This time Gensai identifies him and orders him killed. He has a narrow escape as Kazeba rescues him. She tells him Gensai knew who he was all along but was using him to lure Shintarō into a trap. Sakuzō attacks Shintarō in his hut, is bested and runs out. Seihachi arrives and says he has killed Sakuzō and will guide him. Shintarō notices there is no blood on his sword then Tonbei and Kazeba turn up saying Seihachi and Sakuzō are both Koroku in disguise. Koroku is killed in a fight , leaving them free to cross the mountain.

Now in Owari, Tonbei and Shūsaku are disguised as strolling players as there is a price on Shintarō’s head of 100 pieces of gold. They follow the Retired Lord to the "Black Mansion" where Kazeba works disguised as a maid using the name Namaji. The Retired Lord wants a progress report on the capture of Shintarō. Gensai tells him that Kazeba is helping Shintarō. The Retired Lord tells him that once he becomes ruler, Gensai will be made Master of the Guards but he must kill Shintarō first. "I, Gensai, will stake my life on it." Tonbei infiltrates the mansion and uses a speaking tube to communicate with Namiji as she lies in the maids’ dormitory. The agreement will be presented on the 20th of the month when all the lords are gathered to pray for the shogun. Kazeba offers to find it but Tonbei fears she will be caught. Both are unaware the Retired Lord is spying on the maids. Tonbei is followed by a Black Ninja and is rescued by Shintarō. Tendō the Dragon boasts that if he had dealt with him instead of the others, they would still be alive. He captures Shintarō and Gensai comes to take revenge for Shintarō’s having killed so many ninja. Becoming enraged at Shintarō’s calmness, he tries to kill him by throttling him with his artificial arm. Tendō tells him to leave him alone. Kazeba searches the Retired Lord’s rooms and sees him enter a secret passage and Hakuunsai come out. Gensai becomes impatient and Tendō tries to restrain him. Gensai challenges him but Hakuunsai arrives. Shintarō says he allowed them to capture him so someone else can steel the agreement. He frees himself and in the fight, Tendō is killed and Hakuunsai and Gensai escape. Meanwhile Kazeba has the agreement but is mortally wounded while escaping and dies before she can tell Shintarō the truth about the Retired Lord. Hakuunsai retrieves the agreement. Both Shintarō and Shūsaku are upset by Kazeba’s death.

Gensai gives his men a pep talk on killing Shintarō as the Retired Lord is leaving for Edo the next day. Shintarō, Tonbei and Shūsaku are hiding in a temple. There are Black Ninja patrols in the town, questioning everyone. The temple is attacked and Tonbei remains behind fighting to allow the others to escape. He is wounded and captured, then claimed by Gensai in the name of Sadayori, the Retired Lord. The Chief Retainer of the Owari clan, Fukano, learns of this and goes to Shintarō to let him know he is not in agreement with Sadayori’s plot. He further says that Shintarō can come with him to Sadayori’s mansion when he goes to beg the lord to give up the plot. He affirms that Sadayori’s son, Naritomo, who is the current lord, refuses to have any part of the plot, either. Shintarō rescues Tonbei who tells him Gensai is to kill Fukano. Shintarō intervenes and retrieves the agreement . He and Gensai duel. Gensai leaps a great distance to attack Shintarō but takes a bad head wound from Shintarō’s sword. He says that Shintarō will die with him and pulls off his artificial arm which contains a bomb and runs toward him. Shintarō moves aside and he runs into the river and is blown up. Shintarō confronts Sadayori with the agreement and identifies him as Hakuunsai. When Sadaoryi charges him with protecting the shogunate, Shintarō says he is not concerned with defending the shogun but with protecting the peace because power struggles disturb it. Sadayori asks if he will take the agreement to the shogun because if so, the Owari clan will be destroyed. Shintarō replies that this is not his desire. Sadayori takes all the blame, the plot was his alone and the Owari have not rebelled and he has no wish to jeopardise the clan’s position. Shintarō says he will see that the Owari clan remains as it is. He leaves with the agreement and tosses it unopened into the river. All return to Edo where Shintarō observes it is now autumn. As they walk along the river, t