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Tear Jerker: Eakins Hard Reset
Twilight describing to Celestia how horrible each of her deaths were and how alone she felt every time it happened, before telling her what it must have been like for her friends.
Twilight: All my friends died alone.
Luna's death, which ends up being the final straw in driving Twilight into committing suicide during that loop as that particular future "has nothing left". Celestia's reaction is equally heartbreaking.
Twilight after escaping from the time loop, when she begs Luna to not die again because she can't stand to lose anyone else.
Twilight's reaction in general after ending the loop, when it's clear just how much psychological trauma she suffered from her ordeal.
Culminating in an intervention by her friends where they lay out just how much her refusal to tell them the full truth about what happened to her is hurting them as well as her.
Twilight being forced, due to the effects of Changeling venom, to tell Azalea every single horrifying detail of her trip to the alternate universe, aware that she's being controlled and unable to stop it or even hint to Azalea that she should interrupt her.
And of course, in the companion story The Reign of Queen Twilight Sparkle, it is hard not to feel sorry for Queen Sparkle when, after she finally sees what she's done, and feels incredible guilty, if given hope by Twilight Prime that she can finally die; no more loops. She rushes to say her apologies to the now deceased Luna, and kills herself. What happens next? "Well, that didn't work."