When Chiyoko "Choco" Kurotori attempts to summon Cupid with a stuffed nose, she instead summons the black witch, Gyubid, who decides to train her to become a black witch. Her first job involves investigating a ghost roaming around her school.
When the school decides to hold a cycling rally, Chiyoko asks for Gyubid's magical help to compensate for her inability to ride a bike.
Chiyoko finds herself in a middle of a psychic debate between two boys over the existence of psychic powers, both of which want to date Chiyoko should they win their argument.
Perverted classmate Naoki Kojima takes an interest in a new transfer student, Lulu Ramon. However, Gyubid suspects Lulu to be a spirit attempting to sacrifice Naoki in order to become a black witch.
Chiyoko finds her classmates have been turned into cats by an evil peddler who wants to make them his familiars.
While shopping in Harajuku, Chiyoko and her friend Megu are approached by a supposed model scout. However, this scout appears to be more than meets the eye.
While on a field trip, a girl named Rio Mukai is lured into a house by a witch named Baba Yaga, and it is up to Chiyoko and Gyubid to save her.
As one of her classmates helps prepare something for a picnic, Chiyoko ends up giving him an ingredient from the spirit world which causes everyone who eats the food to go love crazy.
Chiyoko's friend Rinne asks her to help get rid of her bad luck.
Chiyoko and a select few are invited to star in a TV wizardry show. There, she meets a former classmate of Gyubid's, Angolmois, who wishes to make Chiyoko her student.
Wanting to help her classmate Touko Miyase relax, Chiyoko gets Gyubid to help turn her school into a hot spring inn. She soon learns her classmate, Kyou Oogata, is really a wizard trained by Angolmois.
As Chiyoko's class goes on a trip to the beach, a strange being from the Spirit World named Akuma Joe warns Chiyoko that the bus will explode once it reaches the end of the tunnel. In order to save everyone, Chiyoko chants a spell putting everyone inside the Spirit World, where she must play the role of Cinderella in order to escape. As Chiyoko struggles, Gyubid appears to help her get to the ball.
As Chiyoko continues through the story, she and Gyubid discover the culprit is Kyou, who vows to conquer the Spirit World and make the entire class his pets. However, Chiyoko manages to get everyone to return home safely.
Chiyoko is asked by Megu to take her cousin, Momo, to the mall. Whilst at the arcade section, Momo coaxes Chiyoko's friend Touko Miyase into winning a mysterious hand puppet for her siblings. As Touko's siblings suddenly go missing, Momo is revealed to be Gyubid's underclassman, Touka Blossom, who is plotting to sacrifice Touko's siblings to summon a demon.
Chiyoko manages to reveal that Kyou is behind the incident. Touka reveals she was only pretending to be manipulated so she can try and seal away Kyou's powers once more using the puppet. Kyou attempts to have his cuckoo minions steal the puppet, but Chiyoko, Gyubid and Touka manage to recover it and place it on his hand again, sealing his powers once more. Afterwards, Touka starts living in Chiyoko's house to continue her black witch training.
On Class Observation day, Gyubid disguises herself as Chiyoko's mother in order to investigate her teacher, Mr. Matsuoka, who's been possessed by a demon. After exorcising Matsuoka, they discover the culprit to be Akuma Joe, who was accidentally swallowed by Matsuoka.
As the class prepares for Sports Day, they hold a contest for who will be at the top of the human pyramid event. As athletic Suzuka Suzukaze sails through the contest, Gyubid deduces she is a black witch student. Chiyoko and Gyubid tail Suzuka to a hospital as she meets with her instructor, who desires Suzuka to perform a ritual in exchange for her brother's success in undergoing surgery.
Come Sports Day, after Gyubid casts an unknown spell on her, Chiyoko spots Angolmois speaking to another man, Count Leonare, about the purposed ritual, learning the truth that perfoming the ritual will not help Suzuka's brother. Before Chiyoko can warn Suzuka, Angolmois uses paralyzing magic to prevent her from interfering with the ritual which Suzuka begins to perform atop a human pyramid. However, the ritual fails as Suzuka's magic had mysteriously disappeared. As Suzuka's brother's operations goes smoothly, Chiyoko learns from Touka that Gyubid had used a forbidden magic to sever Suzuka's pact with Angolmois, the punishment of which is becoming trapped in a tree in the Spirit World.
In the run up to halloween, Chiyoko learns from Touka that police from the Spirit World are hidden throughout the town, meaning Gyubid is still around town somewhere. They manage to find her in an antiques store. They are confronted by the Spirit World Police, but are aided by Akuma Joe, who tells of a conflict between the Public Magic School Gyubid graduated from and the Black Witch Academy, who got the police on their side. Feeling guilt for allegedly causing her school trouble due to her actions, Gyubid decides to travel to the Spirit World to help her school, with Chiyoko and Touka deciding to come along.
Upon arriving in the Spirit World, the gang, joined by Exnome, go to see Gyubid's principal, Melusine, who assures Gyubid that what she did was the right thing. As Gyubid and co try to escape into town, Chiyoko becomes separated from them and is forced to transform into a dried frog to avoid capture. However, she forgets how to transform back but is luckily noticed by Gyubid before she ends up getting eaten. Just then, they are caught by Leonare and the Spirit Police, where it is revealed that Exnome had betrayed them.
As Gyubid is put on trial, Chiyoko receives evidence from Melusine that can prove Gyubid's innocence. With help from Touka and a few others, Chiyoko breaks out of prison and arrives at the court room, revealing a letter Leonare wrote explaining how Gyubid was set up by him and managing to get Exnome to testify about its authenticity. After Leonare is taken into custody, the judge decrees that Gyubid should not leave Chiyoko's side until she graduates as a black witch.
As Gyubid brings up some magic cards that bring proverbs to life, a grammatical error on Chiyoko's part leads her, Gyubid and Touka to become transformed into dogs. As the card that can change them back ends up being taken by a crow, the gang chase after it. Chiyoko gets seperated and meets Megu's pet dog Gumi, who ran away from Megu since he didn't want to wear silly clothes for a dog fashion show. They eventually manage to retrieve the card and return to human form.
Chiyoko and Gyubid investigate reports of a ghost hanging around the school pool. Finding the ghost to merely be Naoki pulling a prank, Gyubid plans to do a revenge prank, only to find there is an actual monster lurking in the pool.
Chiyoko, Gyubid and Touka soon discover that the culprit is Kyou, who has once again unsealed his powers. Chiyoko manages to perform a spell to cleanse Kyou's heart, although as a side effect she loses all of her manga. After the encounter, Gyubid arranges for Kyou's family to move in next door so she can keep an eye on him, with Touka acting as his little sister.
Chiyoko is asked to investigate a supposedly possessed library, which changes the contents of its books to be about trees. They discover the culprit to be one of Chiyoko's schoolmates who became possessed by a tree demon, which Chiyoko and Gyubid soon exorcise.
After learning a time control spell from Gyubid, Chiyoko attempts to use it to skip a PE lesson. However, after a bug messes up her finger motions, she ends up stuck in an infinite loop where she must do her PE lesson over and over. After going through multiple loops, she manages to break out of it after managing to do a successful vault.
As a cake contest is held, Gyubid teaches Chiyoko a duplication spell to make a copy of herself to look for rare chestnuts for a mont blanc. Things soon get awkward as the copies start making copies of themselves that deviate further from the original with each duplication, so Gyubid and Chiyoko set off to capture all the copies.
As Gyubid grows suspicious of Ogata purchasing a large amount of rice bowls, she and Chiyoko discover him bargaining with a banshi from the demon world, presumedly as a soldier for hire. After they step in to confront him, they learn from Touka that the banshi is actually a chef who Oogata asked to teach him how to make a mont blanc.
Chiyoko gets dragged in by her friends to investigate the curious behaviour of their teacher, Matsuoka. After talking with Gyubid, Chiyoko fears that he may be engaging in a ritual to summon a demon. As it turns out, he was just learning how to make soup in secret.
As Valentine's Day approaches, Gyubid inadvertently feeds the chubby Iwata a herb that makes him seem attractive to everyone. This, Chiyoko must try and give him some chocolate with an antidote whilst facing up against all the other girls that are now infatuated with him.
A strange occurrence appears to be interfering with the class photo shoot, which is soon revealed to be Ruru, who was inadvertently summoned by Gyubid in a magical game of shiritori.
Ruru attempts to get revenge on Gyubid and Chiyoko by putting Naoki in harm's way so Gyubid will get expelled. With help from the class's otaku nerd, Chiyoko and Gyubid use the magical shiritori game to summon ingredients for an exorcism.
