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Tear Jerker: X/1999
Where to start?
Karen's backstory is kind of heartwrenching. So's her death, in the TV series.
Seishirou's death and the aftermath of it. That's all.
Kotori's death made this troper cry so much in the manga. It's not much better in the anime, either.
This troper, who saw the movie first, still cried at every death and Face-Heel Turn, but absolutely wailed at the end of the TV series when she saw the different finale.
Kamui: So... I'll die... and entrust my wishes to you...
And let's not forget the TV series scene that has Subaru recovering from the Angst Coma that he had after the death of Seishirou, risking his life via Taking the Bullet for Kamui, and then telling Kamui to not give up on his wish before he almost dies. SNIFFFF.
Saiki's, Nataku's, and Inuki's deaths were all very upsetting (but the last one comes back, so it's okay).
Nataku's death is even more upsetting in the manga, where he dies in an Heroic Sacrifice to save his "mother figure" (Karen) from his "father figure" (Fuuma), thus fulfilling his Wish. Even Fuuma can't help respecting that as he explains Nataku's reasons to Karen and then spares her for the time being, and Karen mourns Nataku's death.
Sorata's death was saddening in the anime, and it was made even worse when Arashi paid a visit to the shrine where he came from and saw what he wrote for her, placing her head against it.
Alas, Poor Villain: Satsuki's, Kuzuki's, and Yuto's deaths. Specially Yuuto's, in both film and anime: in the first one he's killed in one of the worst ways EVER in the film, and in the second he dies from the injuries Karen inflicted him before she also kicked it, recalling his chat with Satsuki about death and mourning. And lamenting that he won't be able to join her and Kanoe for tea.
Kakyou Kuzuki is a freaking walking tear jerker. If anything, he was already a woobie in the manga but the anime amped this Upto Eleven upon making him an Ascended Extra in the OAV — not only it explains his backstory and reasons, but it shows him trying to save his girlfriend Hokuto before Seishirou offs her. And not only he fails, but he gets shot for all his trouble.My God...