On a wild, stormy night, a group of Fūma ninja infiltrate Edo Castle and steal the Water Tiger mirror. No one knows who they are, or why they stole a mirror. The guard they killed looks as though he met with an accident when a wall collapsed on him. However, he left a clue in the wrapping around a toy he was going to give to his son. This is the character 'kaze' ('wind' - Fūma means 'wind devil' literally). The Fūma return to the castle and kill a number of Iga ninja "Are they men or devils, running like the wind through the castle, breaking through the ninja wall..." At a temple to Marishiten, Kitobō, the second in command of the Fūma, places the Water Tiger mirror before the statue. Fūma Kotarō, the leader appears and chants, "Water calls wind, wind calls fire, fire calls water". He identifies a stranger in their midst and Shintarō is unmasked, disguised as a Fūma ninja.

Shintarō fights his way out of the temple and is pursued by the Fūma through thick sedge and grass. Wounded, he collapses and hides but as Kitobō nears, he dives into the river. Meantime, 5 days have passed since Shintarō went out and Tonbei and Shūsaku are worried. Outside the house, Tonbei challenges a komusō (type of itinerant priest) whom he thinks is a spy. This turns out to be Shintarō who leads him to the boat which belongs to the man who rescued him. He says he can't return home just yet because for the first time he has lost a fight. They are interrupted by the arrival of the boat-owner's daughter, Kaori. Shintarō says she was the one who saved his life. He tells him he was fighting Fūma ninja. Tonbei returns and tells his group to search for the temple of Marishiten. Meanwhile Kotarō repeats his chant, Water calls wind, etc. before the Water Tiger mirror in order to find the Wind Thunder mirror. He is successful for he sees Kaori's face in his mirror, just as she sees his in hers, which had belonged to her mother. Tonbei comes to the temple of Marishiten unknowing and asks a priest (Kitobō in disguise) if that is what it is and is captured.

Kotarō kidnaps Kaori and demands she give him the Wind Thunder mirror. She refuses. Shintarō takes Kitobō prisoner and offers to exchange him for Tonbei and Kaori but Kitobō says Kotarō would have him killed for less. He tells him the Fūma are the only group who could overthrow the government. Shintarō makes him lead the way to the Fūma hideout, unaware Tonbei has already escaped. Three Fūma ninja attack Kaori's father, Sōshūya, for the Wind Thunder mirror but Tonbei has already taken it for safe-keeping, leaving a glass fake. Shintarō decides to finish the journey to the hideout by boat as it would be harder for the Fūma to attack on water but Kotarō has detailed one of his ninja, Naminosuke, a specialist in water tricks deal with him. The boat is attacked by the Fūma dragon ship, a wooden submersible.

Tonbei returns with his group to the temple to rescue Shintarō and Kaori but realises something is amiss when he sees the carrier Kitobō was in. He returns to the Iga meeting place and prepares for the Fūma attack. Kotarō uses Kaori as bait to lure Shintarō into the temple while the Fūma go to the Iga Ninja Mansion to take the Wind Thunder mirror. Shintarō manages to kill the Fūma ninja holding Kaori in the temple and goes to the Iga Ninja Mansion where he takes on Kotarō in a duel. Both are slightly wounded.

Shintarō disarms Kotarō of his sword but the ninja still has his whip. Tonbei shoots arrows at him but he whips them aside then leaps over the roof. Inside all the Iga are dead. Government officials attack the temple by river and by land. The government officials are defeated but in the skirmish, the temple catches fire. The Fūma escape on the dragon ship and Kotarō decides to go after the Fire Dragon mirror and heads for Sagami province. Sōshūya tells Shintarō the Wind Thunder mirror came into his family because he is a descendant of Kozaki Jinnai, the man who betrayed the original Fūma Kotarō. He supposes the Fire Dragon mirror could be the one given to his wife's younger sister, Koshinjo, a nun in a convent near Odawara. Shintarō and Tonbei decide to go to Odawara. After they leave, a Fūma ninja, Kugustu Yonai, emerges from a vase having overheard everything and kills Sōshūya. At Antoku convent, Shintarō falls into a trap set by Oboro, Kotarō's sister, disguised as a nun.

Tonbei's quick action saves Shintarō who kills Yonai. Oboro and the Fūma withdraw. Shintarō releases a nun from her bonds who tells him Koshinjo has gone to Soga village. They set out after her. Meantime Shūsaku has followed them to Odawara and encounters Koshinjo who carries him as he has injured his foot. They take a variant road back to Odawara through Gongen forest where they are waylaid by Tsubame Dōjin and his spider ninja. Shintarō and Tonbei rescue them and Koshinjo tells him she gave the mirror to Princess Aya, the daughter of Lord Okubo in Odawara Castle. Meantime Kotarō reproves Oboro for not killing the nun she captured, tells her to be heartless otherwise the Fūma ninja will destroy her and her being his sister won't make any difference. She begs for the chance to get the mirror.

Musai, an elderly Fūma ninja, infiltrates Odawara Castle and causes Lord Okubo to fall ill, believing himself cursed by the ghost of Hōjō Ujinao, the castle's original builder. Oboro, disguised as a maid to Princess Aya, Lord Okubo's daughter, tells her she can effect a cure if she goes at midnight to the Sōunji, the temple where Ujinao is buried and prays at his grave. Kitobō and the Fūma capture her and when they realise she doesn't have the mirror on her, Oboro volunteers to go back to her room to get it but she is foiled by the timely arrival of Tonbei , Shintarō and some Iga.

Oboro is captured. Kitobō offers to rescue her but Kotarō says she must be destroyed as she has failed. Kitobō protests as she is Kotarō's sister but he is adamant. Musai approaches Kitobō and asks for time to rescue her, assuring him that Kotarō might be angry outwardly but will be secretly glad. Musai kidnaps Shūsaku and offers to exchange him for Oboro. Meantime, Aya, fearing for her father's life, goes to Oboro in prison and offers to free her if she raises the curse put on him. Oboro agrees and when Shintarō and Tonbei come for Oboro, they find Aya. They still go through with the exchange only Tonbei is disguised as Aya. Kitobō interrupts with the real Oboro and there is a fight. Musai success in pinning Shintarō to a tree and begs Kitobō to run him through in order to reach Shintarō. Kitobō does so reluctantly but Shintarō escapes. Oboro tells the dying Musai Shintarō is dead. With Musai's death, Okubo's nightmares cease.

At an inn in Oiso, Shintarō wonders what the secret of the three mirrors is and sends Tonbei and five Iga ninja to Edo to find out. As they are about to cross the Sagami River, they are ambushed. They take refuge in a hunter's hut near Fujisawa with Tonbei wounded. They are surrounded by Fūma and pinned down. Two attempt to break out to get help but one is killed and the other escapes. Kotarō and some Fūma ninja arrive at the inn at Oiso and set fire to it. They attack Shintarō as he runs out with Shūsaku.

Shintarō ends up on the roof in a confrontation with Kotarō while the inn burns beneath them. The ninja who escaped the hut finally arrives at Oiso, badly wounded and hears that a little boy and a samurai were burned to death in a fire. He asks a man (Kotarō in disguise) to confirm this and he takes him to where the bodies are supposedly. Shintarō interrupts and there is a brief fight and Kotarō escapes with a leg wound as he runs up some stairs. Meanwhile Dōjin and his men continue to surround the hut as the Iga group is reduced to two, Tonbei and Koichirō. They prepare to take a last stand. Koichirō is killed and Tonbei is about to take his own life when Shintarō appears and attacks the Fūma. Kotarō calls his men off. Tonbei mourns the loss of his five comrades.

Kagerō Jinnai boasts he is the most skilled of the Fūma. Shintarō, Tonbei and Shūsaku are returning to Edo and stop at an inn at Fujisawa. Outside, Tonbei duels with a Fūma ninja and eventually kills him. Inside the inn, Jinnai seizes the mirrors briefly in Shintarō's room but is wounded by Shintarō and drops them. He escapes leaving a trail of blood which Tonbei follows up into the ceiling and in a room nearby sees a man asleep in bed who looks exactly like the ninja he killed. An old man in an adjoining room has been injured in the fight. He is desperate to get home to bring his sick grandchild some medicine so Shintarō takes him. Tonbei discovers the man in bed who looks like the dead ninja is dead himself and realises the old man is a ninja. The old man reveals himself as Jinnai and demands the mirrors from Shintarō. There is a fight and Shintarō is surrounded by multiple Jinnais. Jinnai explains all his men look like him. Shintarō takes the two mirrors and tosses them away. The real Jinnai runs to them and is cut down by Shintarō He tells the other men they are now free.

Tashirō, a highly skilled Iga ninja and friend of Tonbei's arrives with a letter from Lord Sadanobu and a history of Odawara. The three mirrors together will lead to a treasure of one million gold pieces. Whoever has the mirrors must go to a temple at Enoshima. Tashirō also has a letter he found outside Shintarō's home from Koshinjo saying she is sick ands wants to see Shūsaku. Shūsaku and Tonbei return to Odawara to find Koshinjo well and that she never sent such a letter. Tashirō takes Tonbei's place in guarding Shintarō, identifying various disguised Fūma as they go, then goes after them to test his skill. On a bridge, Shintarō sees Kotarō in a boat on the river. After asking after Kotarō's health (the reply "As you can see!"), he is invited by the master ninja to talk, in the boat. Kotarō plies him with sake and suggests they find the treasure together, which rightfully belongs to the Fūma. Shintarō declares he is pledged to stop anyone from disturbing the peace and likens the Fūma to the empty sake bottle he tosses into the river. They end up fighting, the winner to take all the mirrors. Shintarō drives off Kotarō and claims all three mirrors. Tashirō returns and they go to a temple on Enoshima while Fūma gather.

Kotarō appears at the top of the steps and says he let Shintarō have the mirrors so he would lead them to the treasure. Shintarō tells him that this temple has nothing to do with the treasure as he had guessed Kotarō's purpose. There is a fight, Shintarō runs into the temple and Tashirō emerges having killed the Fūma within. Shintarō sends Tonbei and Tashirō to Enoshima to look for the hidden temple. With the aid of two children, they find a cave with statues and carvings. Tonbei tells Tashirō to guard it while he fetches Shintarō. Tashiro replies, "Fūma are the wind. No one can see them when they are moving" and Tonbei recognises the voice as that of Kotarō who tells him the real Tashirō was burned to death in a fire two months ago. Tonbei is put aboard the dragon ship. Tashirō takes Shintarō into the cave which is surrounded by Fūma including Kitobō and Oboro. Kotarō manages to grab the mirrors in the fight but Shintarō puts his sword to his throat and demands them back. Kotarō tosses them to him and disappears. The fight continues on the cliffs and Shintarō cuts Kotarō across the forehead. He falls into the sea. The dragon shop rescues the Fūma but blows up shortly afterwards as Tonbei had put gunpowder in it before escaping. Shintarō wonders if that is really the end of the Fūma.