Matsudaira Sadanobu sends eight groups of Iga ninja to investigate the eight provinces of Kyushu following reports of smuggling .Tonbei, Kansai and Unosuke are assigned to Hizen. They infiltrate Shiranui Castle where they discover guns and gunpowder being distributed to other lords but one is wounded, one escapes to Edo and warns Shintarō before being killed while Tonbei searches for his wounded comrade.

Kongō approaches Dōhaku of the Puppet Ninja and offer to help him kill Shintarō. Dōhaku rejects the offer and warns Kongō about interfering. Later Dōhaku in his guise as a puppeteer, kidnaps a young girl to force her mother to put poison in Shintarō 's food, Shintarō having journeyed to Kyushu to find Tonbei.

Genshin sends Dōhaku and Kagehiko to trap Shintarō at the border but he escapes. Tonbei returns to Shiranui Castle, finds the wounded Kansai and rescues him. Shintarō finds them in a temple where they have paused to rest.

Puppet ninja Yamizō attacks Tonbei, impersonates him and leaves him for dead in a river where he is found by Maya and Taimon, both Christians. Yamizō lures Kansai and Shintarō out of the hut where they were staying but Kansai sees him talking to some Puppet ninja when he is supposed to be on watch, realises he is not Tonbei and challenges him. In the fight, Kansai is mortally wounded. Tonbei captures Yamizō.

Kongō disguises himself as a shogunate messenger with a message for Genshin to gain an interview with him. After a brief bitchfest on the respective merits of Kōga versus Puppet ninja, Kongō claims that his real purpose in coming was to kill Genshin and take his place the better to kill Shintarō . He backs off when he sees the trapdoor at Genshin's feet. Shintarō gains access to Genshin, pretending to be captured by Yamizō in his guise as Tonbei. Genshin tells him of his plans to take control of Japan. Yamizō escapes and Genshin realises he is dealing with impostors, drops Shintarō through the trapdoor and pins Tonbei to the ceiling. However, Kongō frees them so he can kill Shintarō himself.

Dōhaku, Kagehiko and Yamizō have captured Maya and Taimon and are using them as bait in a trap. Sumie, a young Iga ninja, claiming to be Kansai's sister, rescues Shintarō and Tonbei rescues Maya and Taimon.. Shintarō resolves to get into the castle to "talk sense" into Lord Shiranui. Maya lends him her cross so he can pass as one of the Christians forced to carry the smuggled guns into the castle.

Shintarō uses the chief minister, Tanba Hyōgo to get an interview with the castle lord. He talks of his plots and tries to tell him he is being controlled by Genshin. He will not listen and becomes angry. Genshin appears and captures Shintarō. The lord wants him executed immediately as a spy as is the custom but Genshin demurs. Sumie and Tonbei mount a rescue mission but Sumie leads him into a trap, revealing herself to be a Puppet ninja, Higure Usuzumi.

Tonbei and Shintarō create and set up a series of notice boards in town calling the Shiranui lord and all who serve him fools being manipulated by the Puppet ninja. This serves to enrage to lord who wants Shintarō killed. Genshin has to obey though he would rather use him as a powerful ally. Genshin also warns the lord of Kongō, a "troublesome man". Tonbei and Shintarō hide themselves on some carts carrying the smuggled weapons but it is a trap.

The Puppet ninja capture Maya and Taimon and hold them on a boat offshore as hostages while Yamizō orders Shintarō (Tonbei in disguise) to disarm. The real Shintarō swims to the boat and rescues the two Christians. Taimon warns him that the Puppet ninja plan to kill all the Christians that night. Watching this from afar, Kongō congratulates Shintarō on a job well done but wonders if he will see through to the real Puppet plan.

Kongō is captured by Kagehiko and Usuzumi who want to kill him for always interfering. However, Genshin has other plans and asks him to kill Shintarō while he carries out his own plans. He does so apparently but Kagehiko and Usuzumi attack him under Genshin's order. Genshijn plans to send the guns to Edo by sea while the lord goes overland. Shintarō arrives and tells them the conspiracy is known and the other lords have pulled out after being talked to by Sadanobu. He succeeds in breaking Genshin's hold over the lord. The Christians help scuttle the boats with the guns. Genshin and Shintarō duel and Genshin is killed.