Seeking vengeance after nearly being slain by ninjas who also killed his wife and child, Fujikido Kenji merges with the spirit of Naraku Ninja to become Ninja Slayer, the ninja that kills ninjas.

After a massive drug deal is interrupted, Arson, one of the Soukaiya's ninjas, faces Ninja Slayer in a battle to the death. Ninja Slayer has his hands full while taking on a techno-ninja named Cloud Buster.

Yamoto Koki, a girl possessed by the Ninja Soul of Shi Ninja, uses her powers to save herself and her friend Asari from a gang attack. Shogo, a transfer student, is bailed out of jail and given an ultimatum.

As Yamoto enjoys an evening out with her friends, Shogo shows up to warn her that the Soukai Syndicate is headhunting her. Sonic Boom makes Yamoto an offer she can't refuse.

After tofu manufacturing plant worker Shigaki loses his arm in an industrial accident, he joins other injured workers in taking revenge against the company. Ninja Slayer continues hunting for members of the Six Gates.

Under orders from Laomoto, Six Gates ninjas Earthquake and Hugeshuriken hunt for the Dragon Dojo, run by Dragon Gendoso, the last real ninja in Japan, so that they can burn it down.

Freelance journalist Nancy Lee goes into the forlorn Furutama Projects to chase down a lead, and ends up finding more than she bargained for. Ninja Slayer's Zen meditation is interrupted by an unexpected surprise.

With information that clone cops are about to be introduced into the Neo-Saitama's police force, Nancy and Ninja Slayer break into a secret cloning mill to put a stop to it, but make an unexpected discovery inside.

Following a series of wild goose chases, Nancy tries to convince Ninja Slayer to help get her inside a Yoroshisan hot water bottle manufacturing plant, so she can hack their systems and uncover their secret files.

With Sawatari and Notorious hot on their heels, Ninja Slayer and Nancy find a secret access point to the plant's mainframe. Nancy tries to gain access to the mainframe, but is met with an unforeseen obstacle.

With the antidote in hand, Ninja Slayer makes his way to the cottage where Gendoso-sensei is resting with Yukano. However, their happy reunion is shattered when Darkninja launches an attack on them.

A yakuza captain interrogates a disloyal member inside a bathhouse, but is interrupted by a ninja dispatched from Yoroshisan. Ninja Slayer rescues the captive Nancy. An old foe embarks on a new quest.

Silver Karasu, a ninja who summarily executes those who commit "tsujigiri," the indiscriminate killing of passers-by, considers his own karmic balance when he is confronted by his own mortality.

With his time running out, Kagi gives Yamoto a crash course in iaido training. The Soukaiya send a ninja and bounty hunter after Yamoto, giving her the opportunity to test her new skills.

When Omura's urban expansion plans threaten to destroy Tottoriville, its residents start an uprising, and block the highway. Resistance agents, including a familiar face, fight back against the ninja Omura dispatches.

Ninja Slayer joins Ikki Uchikowashi in order to watch over Yukano, and to see what kind of organization she has gotten into. The group stops a Soukaiya train, and must contend with a pachinko-ball-shooting ninja.

On the run from the Soukaiya, Yamoto stumbles into a church and collapses from exhaustion, only to be awakened by a ninja wearing a priest's cassock. Dr. Lee is desperate to recover a zombie ninja that has escaped his lab.

Naraki, a student at Neo-Saitama 1st University, meets a woman named Maname at a coffee shop to join in a march against poverty. However, Maname is not all that she appears, and the march takes an unexpected turn.

Just as Nancy and Ninja Slayer put the finishing touches on a plan to finally eliminate Laomoto, Nancy is compromised by an unforeseen band of ninjas. Before his big mission, Fujikido deals with some domestic violence next door.

In events from the previous day, Trufflehog sniffs out Ninja Slayer's hideout, locating his computer with the plans to kill Laomoto. In kotodama space, an entity named Baba Yaga approaches Nancy.

Fujikido gets some much-needed rest at home, with Agata caring for him. Laomoto holds a press conference, and makes a shocking declaration. Ninja Slayer runs into an old rival while storming Tokorozawa Pillar.

Ninja Slayer and Darkninja fight one-on-one. After Laomoto is called away to appear in a live broadcast, two other ninjas appear and encourage Darkninja to take on a different task in Kyoto, saying it is his destiny.

With assistance from Nancy, Ninja Slayer challenges the Six Gates ninjas on his way to Laomoto's castle keep. A strange phenomenon tortures Ninja Slayer's mind with images of the dead, including his wife and son.

Laomoto offers Hellkite a last chance to redeem himself. Ninja Slayer at last reaches the castle keep housing Laomoto, but must defeat the last of his bodyguards before he can finally confront him.

As Naraku Ninja and Laomoto continue their rooftop duel, Fujikido must come to terms with the symbiotic relationship that he and Naraku have. Laomoto strikes back with the many ninja souls that he possesses.