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Tear Jerker: Alive: The Final Evolution
This series deals a lot with death, especially considering that the whole plot starts off with essentially The Happening, well...happening, but it was definitely driven home in two specific places with two specific Kick the Dog moments. This Troper was bawling after reading these chapters of the manga.
Seeing Nami's backstory and exactly why she hates all power users: Her younger brother, who had a heart defect but tried to be tough and protect his older sister anyways, gets killed horribly when he's trapped in a car that Kanon exploded and burns to death while crying out to her to save him.
A case of Author Existance Failure is usually enough of a tearjerker, but what makes it worse is that the creator of the manga wrote the last few chapters in his hospital room during his last days. Reportedly he had already been planning another series before his death.