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Tear Jerker: Noir
Noir had an episode with a retired Soviet general who helped people to atone for his crimes. Bonus points for him having a convincingFreudian Excuse and calmly accepting his fate. Chloe's death is also quite gut-wrenching.
Hey, how can you leave out "Morning without Dawn"? The whole episode just rips your heart out and stomps on it over and over. By the ending with Kirika collapsing to the ground begging Mirielle to kill her, we're right there with her.