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Tear Jerker: Final Fantasy Crystal Chronicles: Echoes of Time
Par for the course in this series. First when you see the flashback of Larkeicus massacring your village two thousand years ago. Then much later in the game, you return home to find only the wispy spirits of Eryll and Waltrill are left, and they say goodbye before disappearing. and And then at the end of the game, when you learn the truth about Sherlotta and you have to effectively kill her.
To put it in perspective, by the end of the game, everyone you once knew, save for one, is dead.