Shintarō, Tonbei and Shūsaku have the three mirrors which they use to uncover a map of the Wind Fort in a cave temple. Watching them is Jinkūrō the Owl, a Fūma ninja, supposedly drowned with the rest. Disguised as a blind masseur he comes to the inn where Tonbei, Shintarō and Shūsaku are staying, poisons Tonbei with a herb which causes paralysis then death and tries to force him to draw the map, which he had memorised. He is foiled because Shintarō, suspecting something like this would happen, had Tonbei unwittingly memorise a false map. Jinkūrō is killed in a duel." At the end Kotarō's sinister laugh is heard as Shintarō and co. realise he isn't dead after all. "Fūma are the wind. Beware, we shall come in the night, we shall come in the day and we shall get the map of that secret treasure - Fūma Kotarō is a deathless ninja," he warns them.

Kotarō recovering from the wound he received in the duel with Shintarō (at the end of "The Secret Cave") is forced to stop at Hachiōji to recuperate. He sends Byakuro Genki after Shintarō. Genki disguises himself as Tonbei and attacks the police forces at Hachiōji so Tonbei gets the blame. Still disguised as Tonbei he gets close to Shintarō with the intention of stealing the map. However, Tonbei penetrates his disguise and the two duel. Genki is killed.

Oboro, Kotarō's younger sister, pursues Shintarō and his party from Hachiōji and steals Tonbei's water flask. Tonbei goes into the mountains to search for water where Tarōza the Toad is waiting for him. Using Tonbei as bait, he lures Shintarō to him and deliberately allows himself to be cut down by Shintarō. When one of his branch of the Fūma ninja is killed with a sword, that sword no longer has an edge and is useless to the wielder. Kotarō attacks Shintarō who finds his sword no longer cuts. In the duel, he drops the map which Kotarō retrieves. Shintarō falls down the side of the mountain.

Fūma Kotarō and Oboro begin the search for the Wind Fort while Dennai the Bat starts to look for Shintarō. Shintarō collapses from a wound on a mountain road and is helped by an old man and his grand-daughter. The old man is one of the guardians who for generations have kept seekers of the buried treasure from the Wind Fort. With the old man's directions, Shintarō heads for the Wind Fort and finds the map of the Water Castle. Dennai attacks him but their fight is cut short when the old man shoots the ninja. Shintarō is safely reunited with Tonbei and Shūsaku and they continue their journey to the Water Castle.

Shintarō and his party come to the aid of a girl, Namiji, who is being attacked by assassins in the road. She tells him that she is on an important mission and must get to her home province quickly. Seeing that it would be unfortunate if she was stopped, going through the Hakone Checkpoint, Shintarō plans to take her across the mountains around the barrier. On the way, they are suddenly attacked by a group of Fūma ninja. In reality, Namiji is after both Shintarō and the map of the Water Castle as she is actually a Fūma kunoichi, Ayano, in disguise. But even a cunning kunoichi falls to Shintarō's sword.

Kotarō, who has lost five of his 10 Fūma, visits Kokufūsai who had deserted the Fūma five years before. Instead of killing him according to the Fūma code, he tells him to destroy Shintarō. He takes his daughter, Yuri, hostage as guarantee and Kokufūsai agrees. At Kobotoke Pass, Shintarō happens to rescue Yuri from the Fūma. Unaware of this, Kokufūsai takes Shūsaku hostage and challenges Shintarō to a duel. But once he discovers Yuri is safe, both he and Shintarō realise there is no point to the duel and sheath their swords. Kotarō's plan ends in failure.

Having left Shūsaku with the nun, Koshinjo, in the convent at Odawara, to keep him out of danger, Shintarō and Tonbei set out alone. Tonbei comes up with a plan to find out the strength of the remaining five Fūma. He sends Saizō of Iga, posing as a wandering ninja, to ingratiate himself with Kotarō with a false map given to him by Shintarō. Then he lures out the Fūma, one by one, and kills them. First into his trap is Hagakure Tanba, at Ashigara, near the Water Castle.

Having killed Tanba, Saizō reports to Tonbei that he will find out the true colours of the remaining four Fūma. But Oboro overhears his conversation. Knowing the truth, Kotarō uses Saizō to send out an invitation to Shintarō and Tonbei to come to a nearby waterfall, then sends out Oboro. Shintarō defeats Oboro and she runs away. Tonbei discovers a cave behind the waterfall. This is the Water Castle. There they find the last map, for the Fire Tower, but Kotarō, who has killed Saizō, steals half the map and runs off with it.

The Fūma gather at their base in Odawara. They set watches on the three highways and prepare to wait for Shintarō and attack him. Gennai the Phantom, one of the 10 Fūma, in the guise of a sick man, gains admittance to the convent where Shūsaku is living,. There he awaits Shintarō's visit. That night he discovers from conversation with Tonbei where the two are hiding. Immediately, he gathers his men and mounts an attack. But he falls into the trap set for Shintarō and with his dying breath sends a signal to the three remaining Fūma.

At Odawara, samurai with connections with the Hōjō family have begun secret meetings, centred around Jindai Naiki, the castle warden and chief retainer of the Okubo family, the lords of Odawara Castle. When Kotarō hears of this, he sends Kitobō to find out what these meetings are about. When he learns of the reason for the Fūma's activity, Shintarō disguises himself as the retainer and goes to Kotarō but his disguise has been penetrated and Kitobō takes the opportunity to attack the real retainer. Shintarō is in great danger but is rescued by Oboro and manages barely to save the real retainer.

At the Sōunji, the family temple of the Hōjō, the ninth ninja, Kuromaru impersonates the chief priest. He gives Shintarō some tea laced with a paralysing drug. Then he takes Shūsaku and the abbess Koshinjo hostage. He lures Shintarō to the ruins of Ishigaki Castle, weakened as he is by the drug. However, unknown to Kuromaru, Oboro intends to help Shintarō. Under her guidance, Tonbei rescues the two hostages and she kills her comrade, Kuromaru, for Shintarō's sake.

The Fūma plan to revive the fortunes of the Hōjō family by winning the castle warden, Jindai Naiki to their side. They have observed the ambition of the junior minister who wants Kamijiro's position. The last of the ten Fūma, Yaheiji the Typhoon, tells the junior minister that government spies have been coming and going from Jindai's mansion. If he colludes with spies, he will have to commit harakiri. But if the matter is to remain secret, he must press Jindai to support the Fūma. Shintarō hears of the Fūma's plan, kills Yaheiji and rescues the chief minister, but Kotarō steals the rest of the map.

Shintarō and Tonbei follow the Fūma, using a trail of shuriken left by Oboro as markers. Aware of his sister's treachery, Kotarō uses a false trail of shuriken to drop Tonbei into some rapids, and then lures Shintarō, using Oboro as bait, to a small hut where he shuts him in and sets light to it. Then he heads for Hell Valley (Jigoku-dani). Searching for the Fire Tower, he encounters Shintarō and Tonbei whom he thought dead. Even though badly wounded by Shintarō, Kotarō finds the cave of the Fire Tower. By sheer force of will, he blows up the cave and himself and is buried together with the gold.