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Tear Jerker: Last Scenario
Ortas's and Felgorn's deaths.
The Reveal about Phantom/Alexander, plus his death.
The "goodbye" image of Esmerelda and Barasur you can see after completing the game. It's nice to see them so happy... Until you realize that this is the voyage where she gained insane powers, turned into an Omnicidal Maniac and lost her personality...