During the Westernization of an alternate Japan, humans and spirits coexist. However, some spirits have been causing trouble, and the Ministry of Spirit Affairs is established to maintain harmony. Lieutenants Kei Agemaki, Riken Yoshinokazura, and Ganryu Hanakiri are chosen to represent the humans. They are introduced to their female half-spirit partners: Zakuro, Susukihotaru, and twins Bonbori and Hozuki, respectively. While Susukihotaru, Bonbori, and Hozuki are delighted, Zakuro is disgusted with humans and their acceptance of Jesuit ideas. However, she becomes smitten with Agemaki. Shortly after, spirits Sakura and Kiri play around Agemaki, who immediately becomes nauseous and falls over. In private, Yoshinokazura advises Agemaki against working with spirits as Agemaki's fear of spirits is severe. Agemaki believes that he has no alternative because of what his father might say if he learns about Agemaki's fear. That night, Agemaki walks through the manor and is frightened by the spirits. He runs into Zakuro and hugs her. She interprets this as a romantic gesture. However, he asks her to accompany him to the outhouse because he is too scared to go alone. She becomes angry and wonders how she became smitten with a coward. In the morning, the representatives attend a flower viewing. While they are walking, a crowd stares at the spirits and whispers behind their backs. Zakuro points out that they are used to this and tells Agemaki that he is no different from the crowd. Lightning strikes the ground, and the lightning beast Raiju appears. Because Raiju is well-behaved, the spirits are unconcerned. However, Raiju attacks. Agemaki rescues Sakura and Kiri, but is too frightened to run away. The girls fight and return Raiju to a calm state. As the representatives continue their party, the spirits wonder why Raiju lost control.

Zakuro has a dream that she is climbing a persimmon tree. When she picks the fruit, the tree is surrounded by spirits and she falls into a pool. Her mother's voice tells her that she should not climb persimmon trees because they are connected to the underworld. At breakfast, Agemaki offers Zakuro a candle to eat, believing that fox spirits eat candles, however, this enrages Zakuro and she leaves. Agemaki tells Kushimatsu that he was researching spirits because he wanted to understand Zakuro so he could help her as a partner. The representatives are sent to investigate a hotel construction site. However, construction has stopped because a spirit is scaring the workers. Although talking to the spirit is sufficient, the hotel's owner requests that the spirit be exterminated. Reluctantly, they begin searching for the spirit. However, Zakuro leaves Agemaki by himself. While looking for Zakuro, Agemaki runs into a large, shadow-like spirit. It attacks him, but stops short when it sees he is afraid. The other representatives arrive and pursue the spirit. Zakuro tells the spirit that she wants to talk. However, it does not cooperate. Zakuro slices the column, causing the hotel to collapse. Outside, Zakuro explains that the spirit's true, small form is revealed with light. Because of Westernization, the area is illuminated at night. In addition, the spirit's shrine was destroyed by the construction, so it tried to scare the humans away. She laments the loss of human respect for spirits. However, the hotel's owner is upset that the spirit was not exterminated and his hotel is ruined. To compromise, Lieutenant Hanadate offers to restore the shrine and have the hotel built on military land. He thanks a smitten Zakuro for reminding him to remember the other important things

Zakuro and Agameki are left alone in the house while the others are out on investigations and because of that Zakuro is bored and irritated. Before too long, a client comes to see Kushimatsu about a job that he wants to be done. Zakuro jumps at the chance of taking the case because it is about girls that have been spirited away. Though she is reluctant, Kushimatsu allows Zakuro and Agameki to take the case the clients village. Before they leave, Kushimatsu lets Agameki know why Zakuro is so impatient about the case by telling him about how half-spirits are born and the connection to Zakuro. During the investigation, Zakuro begins to hear voices calling her and realizes that this is the same voice that lured the girl away from the village to be spirited away. That night, Zakuro and Agameki are asked to sleep in the same room and unlike Agameki, Zakuro is surprised an embarrassed by the idea. When they finally settle down to sleep, Zakuro asks why Agameki has been so cautious around her and Agameki tells her about what Kushimatsu told him. Zakuro tells him about her mother and why she can't let these kinds of cases go. As they sleep Agameki is awakened by Zakuro leaving the room. He realizes that she is unconscious and is being led by the voice so he follows her. When she finally awakens, they are in front of a dark cave where a demon resides. They find out that the girls are not being spirited away, but being eaten by the demon. Zakuro defeats the demon and they both leave the cave by morning. Agameki starts to feel guilty about having her always save him from the demons and Zakuro quietly disagrees with him.

Yoshinokazura, Susukihotaru, Hanakiri, Bonbori and Hozuki investigate about a sword in Aya Orikata's possession. Orikata explains that a customer obtained it through "a secret channel" and later noticed everyone around her met with unfortunate events. She gave the sword to Orikata, who refuses to sell it. When Orikata shows them the sword, Susukihotaru begins to breathe heavily and sweat. After, Hanakiri, Bonbori and Hozuki try to locate the customer and leave Yoshinokazura and Susukihotaru to take the sword home. The twins believe the sword was affecting Susukihotaru as she can empathize with objects and other people. At the shop, Mugi, a spirit working for Orikata, shows Susukihotaru a comb. Susukihotaru touches it and sees Mugi and her mother attacked by a swordsman. Susukihotaru learns Mugi does not remember this and tells Mugi that her mother will come if she is good. When Yoshinokazura asks Susukihotaru how she knew Mugi's mother, Susukihotaru admits that she was hiding something for fear of what he might say. Before she can elaborate, Mugi falls trying to take the sword off of a dresser. The sword falls into Susukihotaru's hands, and she sees the sword killing spirits. She draws the sword and attacks. As Orikata protects Mugi, Mugi remembers her mother dying. Yoshikazura catches the blade and cuts his hand, causing Susukihotaru to regain control. Later, Susukihotaru says she does not deserve the concern Yoshinokazura has for her. He realizes her ability to empathize and tells her that because he does not say much, he appreciates her knowing what he is feeling. She cries and tells him that she hopes he knows what she is feeling. Hanakiri and the twins return unsuccessful, and the group leaves for home. That night, Kushimatsu and Amaryoju wonder if the incident was a coincidence or orchestrated.

Soldiers have been lured away by a beautiful woman who transforms into a spider and kills them, earning her the nickname the Black Widow. Hanadate requests that representatives attend that night's military gala and pinpoint the killer. At the gala, the representatives pair off and split up. Hanadate immediately asks Zakuro to dance with him, telling her that it will be easier to watch the women while dancing. In the balcony, Agemaki tries to hide his jealousy while the twins attach magical petals on the women. They explain that they can sense the presence of anyone a petal is attached to when a twin is singing. When the dance is over, Zakuro is left by herself. She is approached by two soldiers who wish to touch her ears. Although she protests, they tell her that causing a scene will hurt the reputation of the Ministry of Spirit Affairs. Before the soldiers can touch her ears, Agemaki intervenes. As Zakuro cries, Agemaki tries to comfort her. The twins notice that Hanadate is leaving the ballroom with a mysterious woman. Shortly after, a petal has been destroyed. Hanakiri and the twins track the destroyed petal and discover Hanadate is trapped in a giant web. The other representatives are confronted by a pair of cloaked figures, but the figures are quickly overpowered. The Black Widow attacks Hanakiri and the twins with her spider form. Hozuki protects Hanakiri while Bonbori fights. However, the twins are only at half of their power when separated, and Bonbori is easily defeated. Before the Black Widow kills her, Zakuro arrives and stabs the Black Widow, who reverts to her human form. The Black Widow tells Zakuro that everything will be explained soon and reveals that she knows Zakuro's mother. Before Zakuro can question her, the Black Widow disappears.

Zakuro asks Kushimatsu about her mother but ends up being said that she will not know about her mother until the right time. While Susukihotaru was telling Agemaki about how Zakuro and the others met and how she looked at them when they first met. After that Agemaki asked if he could go to her room so she thought that it was just look at a girl`s room but is actually to get the kite stuck on the tree near her room but he could not reach it. Then Zakuro asked why he did not climb the tree so he tells her that his afraid of heights and so she is the one who climbed up the tree ,after she got the kite she suddenly heard her mother`s voice and climbed higher until she fell and broke her pendant that her mother gave her and so Agemaki fixed it and put it on her while touching the pendant while Susukihotaru was shocked because no one but Zakuro has touched her pendant.

Tae, a servant in the Agemaki household, comes to the Ministry to send Agemaki home. He agrees to go, but begs Zakuro to come with him. However, she must hide her ears. As compensation, Agemaki must buy her candy later. Once at the house, Zakuro asks Agemaki is he brought her to the house to investigat a spirit. Agemaki is surprised that a spirit still resides in the house. The pair are called down to dinner, where Zakuro learns that Agemaki's father wholeheartedly supports Westernization and is greatly prejudiced against spirits. She also notices that Agemaki's sister is feeding a cat. He explains that when he was younger, a spirit frightened him. His father scolded him for being afraid. Later, Agemaki noticed that his cat, Itsue, was missing. Although he promised to apologize for whatever he did wrong or give up some other treasure, Itsue never returned. Zakuro tells Agemaki that Itsue has always been in the house. She asks Itsue to change form and appear to Agemaki. When Agemki can see Itsue, he finds that she was the spirit that frightened him. Zakuro explains that when a cat is loved, it becomes a cat demon. Itsue simply wanted to thank Agemaki for being kind. She notes that most humans cannot see Itsue in her original form, but there seems to be an exception. The next morning, Agemaki's mother apologizes for her husband's discourtesy, hinting that she realizes Zakuro is a spirit.

While buying a present for Zakuro, Agemaki runs into Susukihotaru, who is returning Orikata's enchanted sword by herself because Yoshinokazura is cleaning shelves. Outside of Orikata's shop, the two cloaked figures they encountered at the gala appear and uses sleeping powder on the pair. At the ministry, Orikata and Mugi tell the representatives that they found Agemaki's gift and the sword outside her shop. Zakuro wants to rescue them, but Kushimatsu refuses to let her go and locks Zakuro in her room. Lord Amaryoju tells Kushimatsu that she can do nothing against the Villge of Oracles and orders her to let Zakuro leave. Meanwhile, the rest of the representatives let Zakuro free, and she and Yoshinokura set out. Agemaki and Susukihotaru wake up and learn that their captives are luring Zakuro out on the orders of Lady Rangui, the Black Widow. Zakuro and Yoshinokazura find where Agemaki and Susukihotaru are being held and are attacked by the cloaked figures. The figures reveal their identity as half-spirits. They tell Zakuro that the rain will soon flood the basement her "loved ones" are being held in, drowning them. Infruiated, Zakuro gravely injures the twin with markings. A magic seal bearing Rangui's image appears and takes the twins away. Zakuro and Yoshinokazura are able to rescue Agemaki and Susukihotaru before they are killed. They return home. There, Agemaki apologizes for making Zakuro worry. Although she claims she was not worried, she cannot stop crying. The twins return home with Rangui. When the twin without markings, Daidai, is gone, Rangui expresses her disguist for her. As she treats the other, Byakuroku, she states as long as Byakuroku serves her, Daidai will be treated as Byakuroku. As she is healing, Byakuroku expresses her anger at the freedom and happiness that Zakuro has.

The three maids are curious about the relationships between the representatives. The twins tell them that human girls play kokkuri to answer such questions. At the same time, Hanadate reports that a strange spirit appears whenever kokkuri is played. Although it has not harmed anyone, he wishes to prevent future damage. So, the group decides to play the game. When they begin, a spirit-like being appears, however, it is just a visualization of the feelings of humans who mistook it for the kokkuri's appearance. The maids and the twins immediately ask it questions about Agemaki's romantic interests. Zakuro does not want to know the answer and tries to stop the kokkuri, causing it to flee. In the courtyard, she attacks it with her blade with no effect. Before it escapes, they hear a voice asking about love. Lord Amaryoju believes that the kokkuri will disappear after witnessing a demonstration of love. However, the love does not have to be genuine. Feeling that he must help, Hanadate accompanies Zakuro and Agemaki. The three of them find the kokkuri. Agemaki begins to say he loves someone, however Zakuro stops him because she does not want him to say something he does not mean. Impatient, the kokkuri charges toward Hanadate. He professes his love for Zakuro. She replies that she loves him, and the kokkuri disappears. Zakuro thanks Hanadate for lying, but he insists that he is a poor liar. Later, Susukihotaru and the maids ask Zakuro if she loves Hanadate or Agemaki. Angry, Zakuro states she is confused because of them. Agemaki realizes Zakuro does not mean what she said to the kokkuri, but he does not understand why he is depressed. Elsewhere, Rangui tells a masked man that he is lying when he describes himself as a poor liar.

At a festival, the representatives pay their respects to Lords A and Um, a pair of komainu-like spirits. When A and Um ask Zakuro and Agemaki are lovers, she denies it. After, the representatives race each other through the festival's maze. Zakuro refuses to go with Agemaki, but they run into each other in the maze. Agemaki wants to apologize if he made Zakuro angry, but she insists that she is not angry. Eventually, Zakuro admits that she does not hate humans. Agemaki takes her hand and leads her. When he asks her if she knows how he feels about her, she runs away. Soon after, she is surrounded by light. Elsewhere, Rangui tells the masked man that she captured Zakuro. Zakuro dreams that she is in a flower field with her mother, who is taken away by small, black spirits. She awakens to find she is shackled to a bed. The masked man enters and reveals himself to be Hanadate, whose true name is Omodaka. He tries to kiss her, but she pushes him away. Zakuro wishes to return home, angering Byakuroku and causing her to cough violently. Zakuro learns that Byakuroku's body suffers when she uses her powers and gives some of her powers to restore Byakuroku's health. Later, Omodaka, sensing that Byakuroku has Zakuro's power, kisses and embraces her. He is confident that Zakuro is perfect for bearing his child. The representatives learn Zakuro is at the the Village of the Oracles. However, they cannot enter the Village because it hovers outside reality. Rangui, infuriated that Omodaka prefers Zakuro, tries to kill Zakuro, breaking the shackles and allowing Zakuro to escape. Upon locating Zakuro, Byakuroku tells her that many female half-spirits are imprisoned because they resemble a powerful half-spirit, Zakuro.

Zakuro finds her mother and once touching her sees into her memories.

Zakuro finallly learns the reason of her birth and of half-spirits. She is captured again and meanwhile, Agemaki and the other members at Spirit Affairs dash off to save Zakuro, armed with the slightest of clues. With the guidance of Lords A and Um, they reach the Village of Oracles. Once reaching there Agemaki hears Zakuro's mother voice and listen to the message she wants him to give to her children. At that time the others find Zakuro with Omodaka in a marriage ritual they stop, so he runs a plce where he can impregnate Zakuro.

With Byakuroku leading the way, Lieutenants Agemaki, Yoshinokazura, and Hanakiri and the half-spirits Susukihotaru, Bonbori, and Hozuki arrive Will the unconscious Zakuro remain in Omodaka's hands. The time of reckoning is at hand. A brilliant final episode to provide stirring and emotional closure!