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Tear Jerker: Pokémon Heroes
See Killed Off for Real on the main page. And it wasn't enough that Latios faded away right in front of his devastated little sister. No, we have to see said sister sight-share with his spirit and watch from his perspective as he drifts away from Earth and vanishes altogether.
She may be a villain, but it's hard not to feel bad for Annie when the DMA starts going haywire with her sister/friend/teammate trapped inside. She's visibly horrified and fearful for Oakley's safety. And despite Oakley being The Heavy and an overall megalomaniacal Jerkass, there's a scene where the DMA's visor flips open and she's visibly traumatized by what's happening.