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Tear Jerker: Artemis Fowl
The entire chapter of The Last Guardianwhere Artemis is about to sacrifice himself to stop Opal opening the second lock, and he reflects on how he has matured and how 11-year-old Artemis would never have dreamt of risking his life like this. Then Holly tries to sedate him to go in his place...
Most particularly, when Butler catches Artemis (who, need I remind you, has been his sole purpose for god-knows-how-long and who he cares for very much and would do anything to protect) and Artemis is already dead.
These lines from the same book:
Holly: "Please don't hate me forever, Artie. I couldn't bear that."
Artemis: "I was a broken boy and you fixed me. Thank you."
Artemis's situation in the first book is quite distressing from an objective point of view - his mother is locked in an attic, his father is missing presumed dead and he's alone in a house with no one but a bodyguard for company.
The part where he goes into his (insane) mother's bedroom and she doesn't recognize him only gets sadder as you age.
Holly saying goodbye to Commander Root in The Time Paradox because she never got a chance to during the Opal Deception.