* CompleteMonster: Ezekiel and Manfred. Ezekiel made his cousin Henry disappear through time out of envy of his cleverness, while Manfred is a sadistic hypnotist (and later pyromancer) who enjoys bullying other kids and seeing them suffer.
* FridgeBrilliance: What happens to Amy and Lyell in the series shows the connection they have with each other. [[spoiler: When Lyell is hypnotised, Amy becomes timid and a shadow of herself, and even Charlie comments that it is as if the spell that took Lyell has captured her as well. Both Amy and Lyell are trapped, Amy in her life in Filbert Street and Lyell in Bloor's Academy. After Lyell is awakened Amy becomes much more lively and self-assured and even plays a part in defeating the Bloors and Harken.]]
* FridgeHorror: Mr Pilgrim's absence in the fourth book borders on this when you realise that [[spoiler: he was being held captive in Yewbeam Castle the entire time while Yorath 'borrowed' some of his personality to be able to pass as a teacher at Bloor's.]] It gets worse when you consider what Paton went through in the third book [[spoiler: when he went to Yewbeam Castle to stop Yolanda from coming to the city.]] Paton implies that Yorath 'borrowed' from him, and also implies that it was a tortuous experience. When you think of what Mr Pilgrim went through now, it's enough to make anyone scream.
* FridgeLogic: Why was Mr Pilgrim unable to resist Manfred's hypnotic power in ''Charlie Bone and the Blue Boa''? [[spoiler: Because he'd already been hypnotised and didn't have any will left.]]
* MoralEventHorizon: Each villain has one.
** Manfred Bloor passes this when he hypnotises Emma Tolly and Lyell Bone, making them forget all their memories.
** Yolanda gets this in the third book when she hypnotises Mr Boldova and wipes away all his memories.
* ShipTease: Emma/Charlie in the third book, until [[spoiler: Emma's found to have a crush on Tancred.]] Also Charlie/Olivia.
* TheUntwist: Seriously, is there ''anyone'' who didn't guess that [[spoiler: Mr. Pilgrim was Charlie's father]]?
** Book 1 involves Charlie trying to find and rescue a girl who was abducted as a baby and put into a trance-like state. Said girl's life with her foster family is very dull and unhappy, and she cries over it once she comes out of her trance. Also it's strongly implied that the Bloors murdered her father, Mostyn Tolly, not long before the book begins. There is a romantic subplot in the book which deals with Paton asking Julia Ingledew out on a date (which goes disastrously), and Charlie has to try and convince Miss Ingledew to give Paton a second chance. In addition, the beginning of the book implies that Charlie's father may have been murdered by the Bloors years ago (though later reveals show that he's still alive and in a trance-like state).
** Book 2 opens with a boy disappearing from his time and reappearing in another, while his little brother wakes up to find him gone. The rest of the book focuses on the disappeared boy who's being hunted by his now ancient cousin and the evil endowed children and the good endowed's efforts to keep him safe and reunite him with his brother. At one point Henry is captured and imprisoned in a pit, and he's ''not'' in a very good state when he's finally rescued. Also, Charlie's uncle is run over by a car. At one stage Paton actually offers Charlie wine to drink (cider in the American edition) one evening while they're talking in Number 9's kitchen.
** The victim of the Bloors' evil in book 3 is an invisible boy who's been locked in the attics for months (if not years), [[spoiler: and he's in a horrible state when he's finally made invisible again]].
** Book 4 has Billy being adopted by a cruel and sadistic couple, a new teacher who is extremely sadistic and dangerous, and the Bloors trying to create a sadistic and monstrous horse to scare Charlie and make him work for them. [[spoiler: Also Gabriel is hospitalised after trying on a bewitched cape.]]
** Book 5 has the villain trying to ensure that [[spoiler: Lyell never wakes up from his trance]], by bewitching said man's wife into forgetting him and falling in love with the villain. Amy forgetting Lyell causes Lyell to weaken and start dying, which is the villain's plan all along. The villain also plans to take Amy back into the past, essentially making Charlie an orphan.
** And Book 6 implies that Lyell still hasn't fully recovered from being hypnotised, and that
** And finally, Book 8 involves the villains trying to murder Amy and Lyell who are believed to have gone whale-watching.
* TheWoobie: Billy Raven has this ''hard''. Each book introduces some new torment that the poor kid has to go through.
** Lyell could also count, in a way, but more in backstory than in the actual series. His father died when he was a baby, and his mother was a complete JerkAss who probably neglected him emotionally once she realised he wasn't endowed in the way she wanted him to be. He spent a good part of his childhood surrounded by nasty, cold-hearted relatives such as Yolanda and the Aunts, and judging from how terrible a sitter Aunt Eustacia was, one can guess how he was treated. On top of all that, his mother held a grudge against him because of a will and a letter his father wrote to him. He falls in love and wishes to marry, but the Yewbeams don't approve and forbid it. He elopes anyway, earning the ire of the entire Yewbeam family. Then, after just four years married and with a two-year-old kid, he gets hypnotised ''for life'' when he tries to stop the abduction of Emma Tolly and spends the next ten years in a deep trance, unable to remember anything about his old life. In the fifth book, when he's close to awakening, he almost dies because Harken bewitches Amy into forgetting him, and all because the Bloors and Titania don't want him to wake up and remember where he put the box that contains Maybelle's will. Even after his awakening, Lyell is still not completely himself again, with parts of his memory still missing.
** Emma Tolly was abducted and hypnotised as a baby, and lived a dull and unhappy life for eight years with neglectful foster parents. When she finally wakes up from her trance, she cries and says that she never knew how unhappy she was, and that she lived with people who didn't love her. The happiness in her life only starts when she goes to live with Miss Ingledew in Ingledew's Bookshop.