Seven Phantom ninja arrive at the mansion of Matusdaira Sadanobu claiming they have been summoned by him and have run the 364 miles from Kōga to Edo in one day. Though mocked by the Iga guards as country bumpkins, they gain an audience with Sadanobu who knows nothing about such a summons. Even the samurai they say summoned them, Aoi, Sakunosuke, denies any such knowledge. Puzzled and disgruntled they leave and take up temporary residence in a temple while they consider their next move. There they see Aoi and challenge him but their leader, Devil-Fire Densai, realises this not Aoi, but Kongō of Kōga in disguise and it is he who has hired them. They swear to follow him anywhere as he is "the greatest of the ninja" and he tells them to come with him to the Lord of the Night. Later Minbu the Dragon, one of the Phantom ninja, sets upon Kawayama Daizaburō, a judge, and kills him despite Shintarō's attempt to stop him. Dying, Kawayama warns Shintarō to beware the Lord of Night.

The Lord of Night summons the Phantom ninja and explains his plans to topple Sadanobu. Kongo crosses off the first name in the "book of death", Kawayama Daizaburō. Hagenbō and Yamizato set a trap to kill the Iga ninja and Tonbei who are next on the list. They capture three Iga sent to Kōga to see if the Phantom ninja have returned and take them to a temple to lure out the Iga and kill them, aided by Kongō impersonating Aoi in such a way as to cause Tonbei to think the samurai is in league with the Phantom ninja.

Tonbei's subordinate, Gensuke, is sent to find the true identity of Kongō of Kōga, the Phantom chief, in the Edo Castle library but is killed and impersonated by Yamizato Danjō who gives the Iga group false information. and tries to divert suspicion to Lord Mizuno as being the 'Lord of the Night'.. He then attempts to impersonate Tonbei in order to lead the Iga ninja into a trap and kill them all but is foiled by Shintarō and killed.

Kongō decides to leave the Iga aside for the moment and go after the next name while the Iga are busy defending themselves. This is Kaizuka Mino no Kami, the chief magistrate of North Edo (kita machi bugyō). He sends Hagenbō and Minbu to kill Kaizuka. They almost succeed despite Shintarō's careful plan to fool them but his sword skill prevails and he is able to defeat Hagenbō's "human steel" technique and lop off his arm, saving Kaizuka.

The Phantom ninja take a doctor to treat Hagenbō and kill him partly so he won't reveal the location of the House of Night and partly as bait to lure out Shintarō and Tonbei by leaving the body in a temple. While they are out, the Phantom ninja kidnap Shūsaku and threaten to kill him if either Shintarō or Tonbei leave the Sainenji (where lives). Chidori makes sure they stay bottled up while the Phantom set about killing the others in the "book of death" by spying on them with her "echo butterfly" technique. However, Tonbei destroys the butterfly and they rush out to find Hagenbō with Shūsaku . He almost kills with his "human steel" technique (and would have if he'd had both arms, Shintarō admits). Hagenbō is killed.

The Phantom ninja kidnap the shogun's nurse, Sakura no Tsubone, from within Edo Castle and hold her in the House of Night. They plan to kill her and leave her body in a public place as a laughing-stock unless she gets the shogun to make Sadanobu resign. However, Shūsaku remembers the way to the House of Night from when Hagenbō took him out to the Sainenji and so Shintarō is able to rescue Sakura.

The Iga ninja set a guard over the captured House of Night in case there is anything within which might give a clue to the identity of the Lord of Night and the Phantom ninja come back to get it. Hitonashi does indeed break in and is captured. He only allowed that to happen so he could get to a hidden compartment and remove a package. However, Shintarō demands he hand over what he took. In the ensuing fight Hitonashi is killed and Shintarō takes the bundle which proves to contain a map of Lord Rokkaku's house. When he and Tonbei go to investigate whether he is really the Lord of Night, they find his house in an uproar and he slightly wounded after an attack by the Phantom Ninja.

The Phantom ninja, now reduced to three plus Kongō, are feeling very frustrated that so many of them have died yet they have been successful in killing only one person in the "book of death" Samunba begs to take the next victim, Izumiya, a rice merchant and purveyor to the government. Izumiya has 10 ,000 gold pieces to deliver to Edo Castle. The Phantom intend to replace the gold with gunpowder and blow it up once it is in the castle treasury.

The Lord of Night wants to have gaol-break of the prisoners in Denmachō prison so they will commit crimes and disturb the peace of Edo in order to bring about Sadanobu's downfall. Kongō undertakes to get himself arrested by disguising himself as a rōnin and killing and robbing a series of people. Once in the gaol he overpowers a guard, steals the keys and is about to release the other prisoners but is foiled by Shintarō who had recognised his sword style.

Kongō summons Hyōe the Spider, a ninja with special kills, and orders him to kill Shintarō. The Spider uses the lamp in Shintarō's room to light a fuse to bombs below the Sainenji. However, Tonbei smells burning and Shintarō realises it is coming from the lamp. He cuts the fuse. Outside Tonbei fights with a ninja and an old man is accidentally wounded. Tonbei, unaware this is the Spider in disguise, takes him inside where Shintarō tends him and sends for his daughter, Chika. She is a ninja, too, and blows a sleeping drug into the room where Shintarō and Tonbei lie while the Spider moves under the floor below. Shintarō who had covered his face with the futon stabs down and the Spider flees outside. Wounded with a shuriken in his shoulder he leaps into a tree where Shintarō tries to persuade him to come down and get medical help but he kills himself after reminding Chika of the ninja code.

Chika comes to kill Shintarō in revenge for her father but is overpowered by Shintarō with Shūsaku's help. He persuades her to give up being a ninja and live a normal life tending her father's grave. However, Chidori comes to her and praises her for getting close to Shintarō and says Kongō is pleased with her and wants to give her her father's crest. She goes with her to what she believes is the location of the new Phantom hideout. This is a trap as it is not the real location as Densai tells her before punishing her as a traitor. They fight and she is badly wounded. Shintarō and Tonbei go to the house and are attacked by Densai, Chidori and the other ninja. Chidori uses the blinding snow trick on Shintarō in the house but Chika throws her web on her, allowing her to be captured. She then dies and is buried next to her father.

Chidori is taken to the Iga Mansion and questioned closely but won't talk. Kongō tells Densai that if she cannot be rescued, she will have to die. Shintarō knows she won't talk so disguises himself as a Phantom ninja and rescues her, knowing she will lead him to the Phantom hideout. Densai intercepts her and tells her that it is a trap and that the ninja she is with did not come from them. He sends her on while he fights with Shintarō in revenge for all the Phantom ninja he has killed. Chidori watched by Tonbei enters the real Phantom hideout which is Lord Rokkaku's mansion. Kongō berates her for not realising she had fallen into a trap and tells her she must pay for the mistake. She asks only to cut Shintarō once with her sword. He agrees.. When Shintarō and Tonbei arrive at the Rokkaku's mansion they find his chief samurai, Kurome Monjūrō who lets them search the place and tells them the lord has taken everyone and gone to Hakone. They are attacked by Phantom ninja and during the melee Kurome kills Chidori.

Shintarō, Tonbei and Kurome set off for Hakone. On the way, Kurome intercepts a messenger riding back from Hakone who tells him that Rokkaku has been kidnapped. The messenger is killed by a shuriken, Tonbei and Kurome fight the ninja while Shintarō rides off. Kongō's disembodied voice tell him Rokkaku and Tonbei are in the forest at Hakone but he will have to face five Kōga groups and if he defeats them, he will have to face Kongō. Shintarō accepts the challenge. Rokkaku tells Densai that Shintarō had nearly discovered his identity. Densai assures him this time is different as they know Shintarō's every move. His men pin Shintarō with ropes but he cuts free. and goes to find Rokkau tied to a tree. Densai puts his sword to Tonbei's throat and orders Shintarō to drop his sword. Kurome appears and cuts him down Shintarō tells Tonbei to get Rokkaku to safety as Kongō is still around but Densai calls out and talks about how Kongō called them from the Phantom Valley and this is how he repays them from which Shintarō deduces that Kurome is Kongō in disguise. And if that is so, then Rokkaku is the Lord of Night. In the ensuing fight, Tonbei pins down Rokkaku who is killed by a knife thrown by the dying Densai. Shintarō and Kongō duel, ending with them both leaping into a boat where Shintarō succeeds in cutting Kongō across the head and he dives backwards into the lake.

This episode was made as a filler before the interruption caused by the Olympic Games later in October 1964. It depicted Tonbei's early life as a young ninja in training and was an extended flashback. It is told in a somewhat post-modern style with Shūsaku asking questions of Tonbei exactly as if he were watching him in the past (or watching Tonbei's home movies). Flashback Tonbei at one point says "Ssh" to Present-day Tonbei as he is narrating. and at another point, looks over his shoulder (towards the camera) and says as if to the future Tonbei and his audience (and the TV audience) "Look at that, it worked like a charm". The "fourth wall" may not have been broken but it was worn awfully thin., Basically this was "everything you wanted to know about ninja" and then some, a kid's dream. On a visit to Iga country, Tonbei tells Shintarō and Shūsaku of his first mission, ten years before, where he was tasked with stealing the plans of Takada Castle from the mansion of Hori Tado. Along the way he describes the different disguises ninja use, the tools and weapons, the methods of disappearing, various ninja tricks and so forth. At the end Shūsaku wants to train as a ninja but Shintarō points out ninja live in darkness, that they belong to a time of war, and Tonbei adds their weapons and skills are designed to sneak into places or kill people. Shūsaku decides he likes the sun too much to be a ninja. . Tonbei says if ever he has a child he won't train him to be a ninja. Shintarō foresees a time when ninja society will collapse and all will be peaceful. Tonbei hopes there will come a time when he can forget every ninja trick he learnt.