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Tear Jerker: Star Ocean 1
This troper had quite a sad feeling after seeing the first part of (the first) Star Ocean, in planet Roark. It's pretty heart-breaking: specifically, the scene when Dorne becomes stone. Just everything about the scene is sad - he asking to lay on his own bed; he giving the little music box to the girl he loves, Millie, seconds before turning into stone... I think the sole reason why this troper dislike the game is because said plot is pretty much forgotten 10 minutes later.
Let's not forget poor Perecci. I didn't like her, but the ending showed her all alone, like she was in the beginning since she couldn't stay in the future with Roddick and Millie. With just her Ocarina. I didn't even like her and I felt like a jerk for that.
How about when you discover Eris' body when you have both Joshua and Mavelle in the party and Mavelle reveals that she's Eris controlling another body, and guilt of what she did while she was Brainwashed and Crazy leaves her Driven to Suicide, and thus Joshua finally gets reunited with his sister just to watch her die. All I can say is, thank god in the remake you that you can keep her from doing this and instead returning to her true body if you also have Ashlay in the party as well.