This is a chronological listing of story arcs, along with brief summaries. For further information, visit the arcs' respective wiki articles (also linked here).
Episodes: 1-3, Sennen Makyō 1
An introduction to the series. This arc focuses mainly on Rikuo's attempts to maintain a normal human lifestyle despite often becoming involved in yōkai affairs. It also includes the event four years prior to the series' start which shaped Rikuo's current beliefs.
The Kiyojūji Paranormal Patrol travel to Mt. Nejireme at the invitation of a supposed yōkai specialist. However, the invitation turns out to have been a trap by the head of the Gyūki Clan. Separated, the members of the Kiyojūji Paranormal Patrol must deal with yōkai of the Gyūki Clan and Rikuo ultimately faces Gyūki himself. Rikuo learns that Gyūki set up the trap because he didn't want the Nura Clan, which he greatly cherishes, to suffer under the influence of a weak leader. Afterward, Rikuo decides to take up the mantle of Nurarihyon and officially become the next Nura Clan head.
On her birthday, Kana is confronted with a Ungaikyō - a yōkai she first met when she was 6 years old. Ungaikyō tries to trap her in a mirror and kill her, but she is rescued by Rikuo's "night" form. Developing a crush on her savior, Kana asks to know more about him and they end up celebrating her birthday surrounded by yōkai at Bakenekoya.
Episodes: 10-12, 14-25
When one of the board members of the Nura Clan is attacked and killed, and Nurarihyon subsequently disappears without notice, the Nura Clan is thrown into chaos. Trying to keep them together, Rikuo encounters a rival faction from the Shikoku area who intend to take over the Nura Clan's territory. Their leader, Tamazuki, is ruthless and willing to sacrifice his subordinates to further his own goals. Rikuo and his Hyakki Yakō battle with Tamazuki and his Hachijūhakki Yakō (consisting of 88 demons, instead of the 100 of a Hyakki Yakō) and emerge victorious, but spare Tamazuki in the end at the request of his father - who Nurarihyon had gone to visit. Tamazuki is spared under the condition that he build a memorial in honor of the subordinates who died by his hand.
Episodes: Sennen Makyō 2
When Kiyotsugu receives an e-mail asking for yōkai-related help, he drags the Kiyojūji Paranormal Patrol (minus Yura) out to help the e-mail's sender, Shinako, who is troubled by the yōkai Jami appearing at her bedside every night. After several incidents, Rikuo figures out that the "Jami" which has been troubling her is a fake and, together with the real Jami, confronts the actual culprits: the priest of the local shrine and the yakuza group working in conjunction with him. The problem resolved, Jami joins Rikuo's Hyakki Yakō and the Kiyojūji Paranormal Patrol return home with Shinako's gratitude.
Episodes: Sennen Makyō 2-3
Ryūji and Mamiru, a pair of onmyōji from the Keikain House, surface in Ukiyoe Town and it isn't long before conflict ensues. Though they came to find Yura, they end up exposing Rikuo as a yōkai and subsequently battling him with the intent to kill. They ultimately have to back down when Rikuo's Hyakki Yakō intervenes and leave after telling Yura to return to Kyoto - as the guardians of two Kyoto seals have been killed by yōkai. This arc is a lead-in to both the Past Arc and the Kyōto Arc.
Episodes:Sennen Makyō 4-5
The story of Rikuo's grandparents: Nurarihyon and Youhime, the creation of the spirit blade Nenekirimaru, and the battle against Hagoromo Gitsune 400 years ago.
Episodes: Sennen Makyō 6-8
When Haguromo Gitsune resurfaces in Kyoto, Rikuo is determined to fight her and take revenge for his father's death - as well as rescue Yura, who has gone to aid the rest of the Keikain family in protecting Kyoto. Nurarihyon, however, is well aware of how dangerous the Kyoto yōkai are and forcefully sends Rikuo to the hidden yōkai village of Tōno to train and grow stronger. Meanwhile, the Keikain House struggles to protect the Kyoto seals from the Kyoto yōkai's forces, with little success.
Episodes: Sennen Makyō 9-24
- Hundred Tales Clan Arc
Rikuo, along with the vast majority of the Nura Clan and several yōkai from Tōno, invade Kyoto. Nearly all of the onmyōji barriers around the city have been destroyed by Kyoto yōkai, and the Keikain House itself struggles to fight against Hagoromo Gitsune's forces. They ultimately join forces with Rikuo's Hyakki Yakō to replace the fallen barriers and stop Hagoromo Gitsune from giving birth to a new evil. After the final battle, Rikuo officially becomes the Nura Clan's Third Head.
After Rikuo's ascension, Tsurara receives control of her own district. There, she helps the Arawashi Clan - who at first only view her as a nuisance - right before the new year. Meanwhile, the Nura Clan celebrates the new year and Saori encounters the yōkai Ganbari Nyūdō, who makes her trips to the restroom a hassle.
Shōei comes to ask Rikuo for advice on a situation in his clan's area of control. The situation turns out to involve a yōkai named Tōryanse the Slasher, who has been spiriting girls away and stealing their faces. Rikuo and Shōei combine forces to put a stop to it, but Tōryanse seems to belong to a larger group - the Hyaku Monogatari Clan.
Ryūji and Yura go to investigate the currently-popular urban legend about a people-eating village. It turns out to be truthful, as they and several of their classmates find themselves facing the village's denizens and the village itself.
When Natsumi stumbles across an artist's studio on a back road, she ends up being used as the model for a new urban legend. A yōkai who looks surprisingly like Natsumi starts appearing on a certain train, and Natsumi herself seems to have vanished into thin air. Anyone who manages to see the yōkai gets dragged into a deadly game of hide-and-seek. Kurotabō rescues Natsumi and Saori, who were both in danger of becoming permanent victims of the urban legend, and has an encounter with Yanagida. The Nura Clan begins to realize that the Hyaku Monogatari Clan is active again.
The story is propelled into the past, where the Hyaku Monogatari Clan's origins and Kurotabō's past come to light. Vying against the Nura Clan under Rihan's leadership, the then-human Sanmoto Gorōzaemon created a variety of antagonistic yōkai using the Hyaku Monogatari. With his death and final story, Sanmoto's body split into 100 parts which become yōkai themselves and caused havoc throughout Edo.
After a prophesy foretelling mankind's destruction at Rikuo's hands, humanity turns against him and tries to kill him. It turns out to be the work of the Hyaku Monogatari Clan, and Rikuo is forced into a game of "Tokyo Tag" where he has to locate and defeat the seven clan executives. He faces the executive Raiden early on and manages to defeat him. Meanwhile, the steps leading toward Sanmoto's revival continue unabated.
In Shibuya, there has been an increase in the number of yōkai present - all of which turn out to be the creations of the executive Kyōsai, whose artwork can come to life. Saori and Natsumi, trapped in a high-rise building with other girls, fight back against Kyōsai in their attempt to escape, but are ultimately unsuccessful. Kyōsai turns Natsumi into a yōkai by drawing on her back, and Rikuo is forced to fight her. Afterward, he finds himself the target of Kyōsai's strongest technique, which causes Rikuo to rot from the inside out.
The executive Tamasaburō, having beaten Kejōrō, uses the latter's appearance to release a multitude of imposters. Meanwhile, Tamasaburō himself heads to the Nura Clan's main house to target Wakana and ends up in an intense battle with Kubinashi. Meanwhile, Rikuo's group are joined by the sudden appearance of Ryūji, and seek out the Hyaku Monogatari Clan's base in order to take out Enchō. When they arrive, it seems that Enchō has betrayed Sanmoto and is planning on reviving the Nue instead. Sanmoto, however, won't be destroyed so easily...
Arc about the Sword Nenekirimaru.
All Youkai gather in the Nura Household.
Hagoromo Gitsune and Seimei revives and the final battle with the Nue and the Gokadoin takes place.