The Lord of Kii dies, his death hastened by the spells of Garyūdōshi who is working for the retainer Naitō Daigaku. Thwarting him is Oribe Hida, who tries to circumvent him by sending a letter to the shogun asking him to confirm Yorikata as heir while Naitō is at the funeral. Genyōsai, leader of the Kishū, is aware of Garyūdōshi's actions. Onkei Onime, Garyūdōshi 's second-in-command forces the maid O-Taka to put poison in Yorikata's tea but Genyōsai knocks it from his hand. Shintarō who has been sent secretly to Kii by Matsudaira Sadanobu rescues O-Taka and her mother from Onime's clutches.

The Kishū take Tonbei and Shintarō prisoner, not knowing whose side they are on. Tonbei escapes and is rescued by the Negoro. Garyūdōshi offers to help him rescue Shintarō and represents his side as the right one. Tonbei is suspicious but accepts their help. This is a ruse to get Tonbei to kill the 6 Kishū so the Negoro can get at Yorikata. Genyōsai challenges Garyūdōshi who reveals his ambitions, to rule through Naitō. They fight and Genyōsai is killed, his body left for the remaining 5 Kishū to find. They swear an oath of revenge at his grave.

Garyūdōshi i sets up a series of challenges, duels between individual Kishū and Negoro with the idea of killing the Kishū off one by one. The first two are the Negoro Hōgen and the Kishū Magojūrō who had grown up together and are friends. They are evenly matched and neither wants to kill the other but Hōgen does succeed in killing Magojūrō. He then goes to Magojūrō's house and tells his young son, Genichirō, that he has killed his father and tries to get the boy to kill him in revenge. Genichirō has been told not to hate the man who kills him by his father before setting out for the duel so resists but finally Hōgen all but flings himself on his sword.

Tonbei is training Genichirō in shuriken throwing when a stray knife hits an old woman. They take her to where they are staying but later that night Tonbei sees her go out and realises she is a male Negoro ninja in disguise. This is the Black Shadow whose face no one has seen. He captures Tonbei and takes him to the Negoro house to use as bait to lure Shintarō there. Shintarō arrives and falls into a pit as he approaches Tonbei. Oil is poured in on him. and the Black Shadow threatens to set it alight so Shintarō will burn to death.

Genichirō who has followed Shintarō, returns and tells the Kishū ninja what has happened and shames one of them, Kurando the Shadow, into going to rescue Shintarō. He succeeds in getting inside the Negoro house and killing many Negoro before he is finally killed by the Black Shadow. When the Black Shadow returns he finds that Tonbei has freed himself and Shintarō is out of the trap and impersonating one of his Negoro, the real guards being all dead. Shintarō sets light to the oil to create light to put the Black Shadow at a disadvantage and eventually kills him. Tonbei and he escape as the Negoro house burns.

Naitō persuades Prince Yorikata to go to Mount Kōya to visit his ancestors' graves over the protests of Hida. Shintarō and Tonbei are sent to Edo with a Negoro prisoner Garyūdōshi deliberately intended to be caught for just this purpose, to get them out of the way. At Mount Kōya, Prince Yorikata is attacked by a practitioner of the Negoro magic rope trick. Shintarō saves him and the remaining 4 Kishū when he cuts the rope and kills the Ninja.

The Negoro attack Prince Yorikata's palanquin on its way back to Wakayama Castle but find it empty. Prince Yorikata has been hidden by Shintarō and the palanquin was a decoy. They use Shinigami, the Deathless Ninja who attacks the party with the palanquin, blinding one Kishū ninja, Sakon. The three others go off after the Negoro while Shinigami pretends to be one of the Kishū and asks Sakon where Yorikata is hiding. Sakon gives him false information because he is suspicious and is killed. Shintarō, Yorikata and Tonbei are on the river and are surrounded by explosions. They make it to shore where they fight the Negoro there, drive them off and apparently kill Shinigami.

Shinigami uses his skills to disguise himself as woodsman and lures the three last Kishū ninja to their deaths. He then traps Tonbei and gives him a paralysing drug. Still in disguise, he runs to Shintarō saying Tonbei is ill and needs help. He guides Shintarō to an abandoned temple and attacks him as he tends Tonbei. Tonbei manages to warn Shintarō that the only way to kill Shinigami is by striking him with the back of the sword, not the blade.

Gohei, an Iga ninja messenger, is attacked by Onime wanting the letter he carries. He falls into a river and is rescued by a woman named Oko. He asks her, as he is too weak form his wounds, to go to the village of Iwamoto and bring Shintarō and Tonbei back to the hut. She does so but reveals herself as a Negoro ninja once Gohei starts to hand over the letter. She takes it and gives it to Onime but it turns out to be a blank sheet. Gohei has memorised the message, which is that the shogun has confirmed Yorikata's succession. Oko swears revenge.

Oko engages a ruthless, psychotic rōnin, Jingo, who happens to be a very fine swordsman to kill Shintarō and torture Tonbei to find out where Yorikata is hidden. In return, he will gain a high position in Wakayama Castle under Naitō. This is her one chance to redeem herself. if she fails she will be killed. Jingo apparently kills Shintarō in a duel and captures and tortures Tonbei. Oko gives Jingo poisoned sake as he has done what she wanted and she has no more need of him. However, he doesn't really drink it and kills her. Shintarō, disguised as one of the Negoro sent out to make sure he is really dead, duels with Jingo and kills him while Tonbei kills Onime.

Shintarō and Tonbei go to the village of Nabari in Iga country as Tonbei's old teacher, Handayū, has hidden Yorikata at Shintarō's request. There they are met by four Iga ninja and Shintarō arranges an ambush at Tenma Temple for the Negoro who are following them. However, one of the four Iga is really a Negoro ninja and starts to kill the others one by one. He is discovered and killed by Shintarō.

Three highly dangerous and highly skilled Negoro ninja monks arrive in Nabari and take Tonbei prisoner as bait to lure Shintarō into the pine forest. There he is wounded in the leg but escapes. Hanadayū's daughter, Kumeno, binds his wound and goes to help Tonbei on his instructions while he stays to fight the monks who are coming. He succeeds in killing them and Kumeno rescues Tonbei.

Handayū ostensibly goes to Yorikata's hiding place, followed by Garyūdōshi and the Negoro but he is leading them away. He encounters Garyūdōshi and they fight, both falling into the river. Tonbei and Kumeno arrive, smell the gunpowder Garyūdōshi was going to blow up Handayū with but see no one except Yorikata fishing further away. He hooks up Garyūdōshii from the river who tries to attack him but Garyūdōshi forces Shintarō to drop his sword. He lunges at him but Handayū comes up from the river and throws a knife into his wrist allowing Shintarō to pick up his sword and throw it at Garyūdōshi, killing him. Handayū dies shortly after, but not before he gives several long speeches, saying this is the fate of a ninja, he's done his duty and that Kumeno should live to help others.