%%* AngstWhatAngst: Lyell recovers surprisingly quickly from being hypnotised, considering that he spent ten years trapped in Bloor's Academy without any of his memories,
* 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.
** There's a ''huge'' ShipTease between [[spoiler: Henry and Ankaret]] in ''Henry and the Guardians of the Lost''.
* TheUntwist: Seriously, is there ''anyone'' who didn't guess that [[spoiler: Mr. Pilgrim was Charlie's father]]?
%%* WhatDoYouMeanItsForKids: This series is darker than most people would expect for a kids' series. For example:
%%** 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 the kitchen in Number 9.
%%** 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]]. There's also what Yolanda does to Mr Boldova...
%%** Book 4 has Billy being adopted by a cruel and sadistic couple, a new teacher who is extremely sadistic and dangerous (and also a scary shape-shifter out to get revenge on Paton for killing his daughter), 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.
%%** Book 6 implies that Lyell still hasn't fully recovered from being hypnotised, and at one point Charlie fears that he'll never again be the brave man who stood up to the Bloors years ago.
%%** 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. [[spoiler: Though he does eventually regain all of his memories at the very end of the series.]]
** 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.
** Paton. His mother was murdered by Yolanda in Yewbeam Castle when Paton was only seven years old; his sisters turned to evil at the same time. His endowment made him a pariah in society and his own family, as he couldn't go outside in daylight. Also because of his endowment he's pretty much a loner, as not many people are brave enough to befriend him. His only friend Lyell disappeared under mysterious circumstances in 1994, and Paton blames himself for it because he didn't meet Lyell when Lyell asked him to. Paton meets a nice lady who he really loves, and who loves him back, but ''something'' always seems to crop up to stop them from progressing their relationship into something more.