Having given up on life, 15-year-old Chise Hatori sells herself at an underground auction, where she is bought by Elias Ainsworth, a not-quite-human mage, for 5 million pounds. She learns that he intends for her to be his future bride, and her world begins to change.

Few people know the truth about the bookstore on the outskirts of London that Elias frequents. He takes Chise there, where they meet Angelica, who teaches Chise a little bit of magic, but... The true power of the Sleigh Beggy materializes a fragment of Chise's memories.

Simon, who is assigned by the Church to keep an eye on Elias, visits with some business. One of his requests brings Chise and Elias to the ends of the earth, where they meet Elias' mentor, Lindel, along with an old race on the verge of extinction. An old one, about to return to the earth, spends his last moments sharing a dream with Chise.

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.

With the church's requests fulfilled, things were supposed to go back to normal. But Elias has been acting strange since the last request: he'd vanished on the first morning after Chise had spent a night in his room. Neither Angelica's kind words nor Ruth's pure words are enough to put Chise's mind to rest.

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.

Elias, is an odd failure who pretends to be human -- but is it because of his master's words, or because of his distrust for humans, that he stopped communicating about himself? Lindel's alias, Echoes, refers to the to a song akin to the sound of snowmelt, traveling through the wind, causing the blooming of flowers and the dancing of fairies. The magic of the song turns into a mirror the surface of the water Chise peers into. What does she see beyond the mirror?

Lindel finishes the staff that Chise had finished carving. As she finishes, she meets an old friend, who offers her some wise advice.

Chise and Elias are in the middle of shearing Wooly Bugs, magical creatures who eat cold from the air and grow wool with magical properties. Chise becomes distracted and is attacked. As Chise recovers, she and Elias open themselves up to each other more.

With Chise being transformed into a fox, she takes off running into the woods. Elias chases after her. Later, Chise is visited by the Leanan sídhe, who is attached to Joel, claiming that Joel will not wake up.

With King Oberon taking Chise into the Fairy realm for recovery, Silke becomes agitated waiting at home. Chise slowly recovers under Dr. Shanon's care, a fairy that was raised as a human.

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

Stella, a young girl Chise encountered while Christmas shopping, finds that her brother, Ethan, has gone missing and her parents have forgotten he exists.

Stella visits Chise with her payment of sweets. Elias, irritated by and jealous of Stella, runs away. Chise finds him hiding in a shadow but becomes worried as he restrains her and seems to want to eat her.

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.

Having captured Chise, Cartaphilus begins grafting parts of her onto himself. He forces her to relive some of her worst memories.

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.