In a mix-up at the photo developer, Charlie Bone receives a mysterious photo of a man and a baby instead of the one he dropped off of his friend's dog which he planned to use for his friend Benjamin's birthday card. Charlie is shocked when he realizes he can hear strange voices of the two in the photo (and the person who had taken the picture), but his other grandma Grizelda Bone and great-aunts are thrilled. They inform Charlie that because of his magical endowment, he can now attend Bloor's Academy. Charlie is placed in the school's music department because his father, whom Charlie believes is dead, had been a pianist.
Charlie then receives a mysterious visit from a man Mr. Onimous, who tells Charlie he was brought there by his three cats.(Aries,Leo and Sagittarius). Mr. Ominous tells Charlie he must go to Bloor's even though he doesn't want to, because that is where the lost baby who was in the photo is. Charlie returns the photograph to its correct owner, Julia Ingledew, who says it is the only picture she has of her long-lost niece Emma Tolly, who was given away to the Bloors by her brother-in-law Dr. Mostyn Tolly in exchange for something that is a mystery to her--a long silver case. To thank Charlie, Julia gives him a robotic dog that plays tapes and the case. To keep the items safe from his nosy aunts and grandmother, Charlie gives the items to his best friend, Benjamin Brown.
At Benjamin's house, Benjamin and Fidelio Gunn (another one of Charlie's friends who tutors him with his music on Sundays) play the tape in the robotic dog, which gives instructions from Dr. Tolly on how to open the case (which is called "Tolly Twelve Bells") and awaken Emma, who would now be the same age as Charlie. Charlie, Fidelio, Benjamin, and his uncle Paton must try to retrieve the missing baby. The girl happens to go to Bloor's, and she is endowed. Her name is Emilia Moon, which is her adopted name. Her real name is Emma Tolly. Charlie asks for the help of friend, and fellow Bloor's student, Olivia, to help get the attention of Emilia (Emma Tolly, the missing girl).
Meanwhile, Benjamin receives an unwelcome visit from Eustacia, one of Charlie's great-aunts(who fed him horrible soup), who believes Tolly Twelve Bells is still hidden in his house (it was at one time, but it was then moved to Fidelio's house). He accidentally makes her believe that the case is in the cellar and his dog, Runner Bean, is guarding it, so Asa, the beast-boy, becomes a beast and attacks Runner.
Gradually it appears that Paton is no longer keeping his head down and he is trying to help Charlie. He is greatly angered by the attack on Runner Bean.
Olivia convinces Emilia, who is quite easily lead seeing as she is hypnotized, to come to Fidelio's house. They open the case, which turns out to contain a tape of the church bells that were sounding when Emma was hypnotized by Manfred Bloor. She is awakened and starts sobbing uncontrollably, realizing that her adopted parents do not love her.
Emma goes back to the Moon household (the Moons are people who the Bloor's are paying well to take care of her, but they do not really love her). The Moons are very angry with her, and say she has 'broken the rules and must face the consequences'. She is dragged to Bloor's, where she is imprisoned in a dark, stone room with only one, high up window. An invisible presence opens the door for her, but she is soon recaptured. She remembers that Charlie said she could fly, and she transforms into a bird and escapes.
She transforms back to a human again, and encounters Paton. They are both going to Ingledew's (Paton really likes Julia, and he took her out for dinner, but his endowment is boosting powers which causes breaking of light bulbs, so all the bulbs shattered and he ran off in terror without paying the bill, and she is really mad). For a few days, Emma and Julia lock themselves in the bookstore, but the Moons were pounding on the door, insisting that they couldn't prove Emma was Emma Tolly without the adoption papers. The Bloor's had them.
Angry, Paton stormed up to the school, and demanded the papers. When Dr Bloor refused, Paton started exploding all the lights. The Bloors didn't want any attention brought to the illegal adoption, so they threw the papers out of the window to Paton. So Emma was with her aunt, and away from the Bloor's. Charlie decides he needs to stay at Bloor's Academy, to help protect people like Emma who is a sad, lonely child that needs to be protected.
|45px||This article about a children's fantasy novel is a stub. You can help Wikipedia by expanding it.|