Long ago, the humans and cats of Ulthar, city of cats, were struck by a great tragedy. For generations, the souls of those who were at the center of this tragedy have been sealed away by the king of cats. Chise and Elias travel to Ulthar in order to complete Simon's second task: to purify the spirits that remain.

To sorcerer Refnred's eyes, Chise is a sad girl, being duped by a mage. But no matter what Elias' true motives are, Chise has no intention of leaving him. Elias was the first person to value her, after all. As she walks towards the epicenter, she learns of the truth behind it. The sight of a boy appears behind the tragedy.

Chise is deep in thought as she watches the souls return to where they'd belonged all along. More than ten days have passed since the incident at Ulthar, but she is still in a deep sleep. Elias and Simon stand worriedly by her side, when they are met by two unexpected guests: Titania, Queen of Fairies, Lord of Tír na nÓg.

The dog, with its flowing, black hair and burning red eyes, called Chise by the name "Isabelle." The Church's final request is to investigate a black dog that emerged in a cemetetry, but the black dog ends up saving Chise from danger. Meanwhile, Renfred's apprentice, Alice, is also on the move, looking for the black dog.

Alice sees Elias' changes and decides immediately that he could never be human. Sorcerer Cartaphilius, who is attempting to capture the black dog by manipulating Renfred and Alice, causes Elias to show a completely different side of himself when his "work" hurts Chise. Those who know Elias call him the Pilum Murialis.

Chise and Selkie climb aboard a dragon's back to meet Lindel, to have her own mage's staff made. Frustrated by Chise's acceptance of her being kept as a pet by Elias, he describes the time he found Elias in the darkness. Meanwhile, Elias, who had stayed at home by himself, receives a letter from a sorcerer's college.

Christmas is coming up. Alice invites Chise out to London, where they hang out together and go gift shopping for Renfred and Elias.

In the land of dragons two young dragons are kidnapped from Lindel by Cartaphilius. Chise awakens from a dark dream to find, Alice, Renfred, Adolf and college administrator Tory Innis in Elias’ home. They explain Cartaphilius stole the two dragons using a teleportation device he stole from Renfred and want Elias to find the dragons and take them home

As the dragon rampages, Elias tells Chise they must absorb the dragon’s magic in order to stop it. This leaves Chise in a predicament as Elias becomes unable to help.

Elias earns the help of many, and they form a search party for Chise. Meanwhile, Chise and Cartaphilus relive his past together.

Cartaphilus and Chise argue over their respective approaches to dealing with their own suffering, beating each other up brutally in the process.

Chise attends her first day at the College with Elias in tow.

It's a day of new beginnings at the College as Chise attends her first day of classes and meets some of her fellow students, and Elias adopts a mysterious guise for his first time teaching as a visiting instructor.

Chise shares a meal with her new classmates, but several teachers and students at the College have their eyes on both her and Elias for reasons yet unknown. Chise and Elias head home for the weekend and Stella drops by for a visit.

Two separate conversations reveal the multitude of revelations that Chise and Elias have had about one another, and the ways they've both grown and changed. Hazel guides them on a dangerous shortcut back to the College.

Chise learns a bit more about the history of both the College and her classmates. Zoe's secret is revealed, and a pact is formed.

Alice and Chise to try and sort through their feelings on their complicated relationships with their respective masters.

Chise attends P.E. as Elias looks on. Philomela is summoned home. Alice stubbornly continues her training, while Adolf consoles Renfred through his troubles. The students embark on a camping trip.

An otherwise educational and relaxing camping trip with her classmates ends with a terrifying encounter in the shadows of the night forest, forcing Chise to rely on her own wits and abilities instead of Elias' magic.

After returning from camp, Lucy is still unconscious and it's still not clear what's behind her sudden loss of strength...this worries Chise deeply.

While watching over Lucy, Chise discovers her connection to Seth and their family's tragic history. While a professor seems to have been the victim of a user of a banned book, a mysterious killer seems to resurface...

Apparently, a forbidden magic book called "The Testament of Carnamagos" is being used to rob Lucy and Simeon of their magical powers. But who exactly is behind it is still unclear. Elias takes care of the matter because he fears that otherwise Chise will put herself in danger for her friend and because he himself wants to protect a friend.

It's time for family explanations, whether between Lucy and her brother, or Alice and Renfred. The College is also going through a complicated period where other magicians seem to want to harm new students.

The College is sealed off to protect the students and staff from whatever or whoever has been sapping magic from victims. Zaccheroni puts the students' survival abilities to the test, but with a catch: no sorcery allowed.

Outside the College, the witches hunt for the missing book. Inside, the students try to juggle lessons with their own personal goals and relationships. Philomela confides in Alcyone, but an ominous message reminds her of her assignment.

Bored with having nothing to do but study, the students play a puzzle game, but it stirs up bad memories for Philomela and Rian. Alcyone ponders her assigned role. As the rainy season starts, Elias and Chise finally sit down to catch up.

Violet and Chise host an after hours test of courage for their classmates by having them pair up to visit various haunted locations around campus, but the evening leads to some revealing conversations.

The mystery deepens as all the students drained of magic suddenly wake up feeling fine. Rumors about the culprit start to rise among the student body. Veronica checks in on Philomela.

Despite their disappointment that the College will be closed through Christmas, the students try and prepare for the holiday party. Chise takes another dive into Lucy's memories. Philomela reaches her breaking point.

Philomela bargains for Liza to undo the seal over the College so she can return home to fulfill her duty. As Chise gives chase, her power gives her a terrifying new form.

Alycone reflects on Philomela's childhood and her all-important task. An ancient and fearsome goddess blocks Chise's path on the way to the Sargant family home and demands tribute that was promised a year ago.

While Zoe fights off the werewolf, the other students finally reach Philomela. Chise takes a dive into her dark memories, but as everyone's secrets begin to unravel, Philomela hesitates to take her classmates' outstretched hands.

As Lizbeth's plans near fruition, Philomela thinks about what it is she really wants.

The fight begins in earnest as Lizbeth starts to gain the upper hand, but Chise and company receive some unexpected assistance.

Philomela stands against Lizbeth in a final battle of wills.