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Tear Jerker: Forsaken
The Legendaries trying to save the world and failing. They would then struggle to fix it up with their immortality and powers stripped away as punishment, and they slowly acknowledge the fact they can die at a moment's notice.
Mew's pregnancy and miscarriage, and the incident that followed.
Amber's backstory even if you knew about it.
In the same chapter, Mew returning home to her body at the risk of losing her memory of Amber.
Mewtwo pleading to God as he tries to revive Mew after she drowned.