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Tear Jerker: Children of the Red King
When Amy and Charlie go to bring Lyell home in Charlie Bone and the Hidden King, they see Lyell in the academy's chapel and Lyell doesn't recognise them. Amy's reaction to seeing Lyell alive and her despairing cry only adds to the emotion.
Tancred's drowning in Shadow of Badlock, and his friends' grief over it.
My Greatest Failure: Paton Yewbeam never really forgave himself for not helping Lyell at the cathedral on the day he disappeared.
Paton goes through this when Ms Ingledew is dying from wearing a bewitched belt. The look on his face when he realises he can't save her is heart-wrenching. luckily Charlie and his wand are able to revive Ms Ingledew.
Heroic Sacrifice: At the end of Charlie Bone and the Castle of Mirrors, Billy Raven's guardian Christopher Crowquill sacrifices his life to save Paton's when Yorath Yewbeam tries to kill him, because he's dying anyway and Paton is the only one who can protect Billy.
The entire scene where Charlie is using the Mirror of Amoret to discover where his father is. After remembering (with Claerwen's help) a memory of Lyell smiling and playing the piano in Diamond Corner, the Mirror takes Charlie mentally to the Music Tower, where Lyell sits slumped over the piano and looks half-dead. And when Charlie calls out to him, he tells him to go away and 'There's nothing left'. Charlie's reaction (a terrible scream) to seeing Lyell almost dead is particularly heartbreaking. It's saddening to see that the smiling man in Charlie's memory has become the dazed, almost dead man Charlie visits in the Music Tower.
The reality that Lyell never got to see Charlie grow up, and that he lost ten years of his life just because the Bloors decided he had to be punished for 'breaking the rules' and trying to prevent the abduction of Emma Tolly.
Every single scene where Charlie meets his father by chance in Bloor's Academy, when Lyell is still spellbound. It's hard not to cry when the reader sees Lyell trying but unable to remember, and Charlie talking to his father without knowing who he is.
Every single time Paton, Charlie and Amy think or speak of Lyell.