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.
Lets be honest, as if resurrecting your girlfriend only to find out that she has to perform a Heroic Sacrifice isn't enough, then finding out that she can't actually do it, and you have to pull the trigger on her yourself has to be one of the most tragic experiences a game can put you through. I cried.