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Tear Jerker: Digital: A Love Story
Emilia is recompiled into the anti-Reaper program and begs you to connect her to ARPANET so she can start her Heroic Sacrifice. Combined with the music and the genuine feeling of isolation at this moment, it's just heartbreaking having to type in its phone number for the last time.
And her last goodbye to you is absolutely heart-rending, particularly if you spent time arguing with her about it, or trying to find another way.