Heartwarming / The Negotiations-verse

Reunited

• When Twilight and Fluttershy reconcile and Fluttershy makes it clear she never once hated Twilight.
• Twilight's inner narration notes that for all the atrocities Celestia committed, the one thing she can't forgive her former mentor for is being the direct cause of Spike's misery. It goes to show how much she cares for him that she'd condemn the one pony whom she admits to having loved even more than her own mother for harming him in such a way.

Rest

• Twilight, an old mare on her deathbed, turns over to see a massive candlelit vigil outside of her home, with humans and ponies alike mourning for her approaching passing and humanity showing they have forgiven her.
• The fact that Discord holds humanity in such high regard and is genuinely captivated by how random they can be, not to mention his fascination with everything they have achieved despite their shortcomings.

Future

• It's a background mention, but the fact that humanity and ponykind have come to peacefully coexist alongside one another in the centuries that have gone by, creating a harmonious society and accomplishing great things together (including fully and successfully colonizing Mars) is touching.
• Spike has become a history teacher, taking Discord's advice from earlier, and he's made a pretty fulfilling life for himself, finding friendships with his students and colleagues.
  • Even when he's dying, Discord spends his last moments encouraging Spike to let go of his fear of being happy and to live life to its fullest so he doesn't die with any regrets.
• The finale: Spike finally puts his fears aside and commits to being with Rebecca, who reciprocates. The two then consummate their new relationship that very night.

Warfare

• For all his Holier Than Thou posturing, Halberd's relationship with Thundershot is genuinely sweet to see. Love really can bloom on the battlefield.
• The finale: although Halberd was ultimately Driven to Suicide as he couldn't handle Equestria's surrender, his family is revealed to have survived the war and later found his journal, which his sister kept as a family heirloom to be passed down to her descendants. It's also revealed that Spike is now engaged to Rebecca and is still as devoted to his mission as ever.

Choice

• "Devastation": Even though they'd just had a vicious screaming argument, Applejack still puts her pride aside to rush to try saving Rarity and Sweetie Belle during the Bombing of Ponyville. She doesn't succeed, but it's the thought that counts.
• "Decision":
  • Discord arrives in Equestria to plead with Celestia to surrender. She, of course, stubbornly refuses, prompting this response from the chaos spirit:

    Discord: You know what? You win, Celestia. I concede. You hear me, you've won. Because it's clear to me that you're set to commit this overly complex method of suicide regardless of how hard I try to change your mind. At this point, I don't care. I don't care what your motive is, or whatever sob story you're holding back that no one, not me, not your circle of confidants or even the whole dang populace knows about. I don't care if you're doing this because of revenge, justice, racial superiority or some warped combination of the three. I don't care that you've decided to stomp and scream about in your room like some snot nosed brat throwing a tantrum after being told no, she can't have candy for dinner. I. Don't. Care. (Beat) But what I do care about is the fact that you're willing to take everypony with you, all over some misguided attempt at... whatever the heck any of this is. None of them have to die. Just surrender.

    • Before he leaves, Discord notes that ever since he learned the value of friendship, he's been happier overall.
• "Division": After the utter tearjerker that was Applejack and Rainbow Dash's argument with Twilight over her decision to surrender to the humans and them venomously calling her a failure and declaring their friendship with her done and over with, Spike (who had been listening in on the conversation) comes out to console Twilight, reassuring her that she's made the right choice and he'll always stick by her no matter what.
• "Oppression": It is revealed that Captain Parabola, who had been taken by the ESS previously, took over the working hours of a mare's son and those of the other prisoners when they couldn't work to spare them all from the forced labor and was given a proper burial by them when he eventually died.

Fallen

• Even though his death is a Tear Jerker, Discord finally confesses to Fluttershy his love for her, something that he was regretfully unable to do in the canon "Negotiations" timeline.
• Fluttershy's unwavering care and love for humans and describing all the kind things humans did for her to the rest of the Element Bearers and Celestia as a counterpoint against their misanthropy.
  • Fluttershy and Spike reconnecting, capped off with Spike defecting to join the resistance and Fluttershy making it clear to him that they never stopped being friends.
• "Divine Justice":
  • Fluttershy is given the choice by Harmony to punish her former friends for their actions during the war and decides to spare them. She may not forgive them all but the thought that they were friends once was enough to make her spare them (though there is a touch of Cruel Mercy in there as well). Even Harmony is impressed by Fluttershy's willingness to take the high road here.
  • As the ponies surrendered before the Invasion of Equestria in this timeline, several characters that died in the original story are spared. We get to see that Apple Bloom married Scootaloo, while Spike becomes mayor of Ponyville and marries Sweetie Belle and they (along with Rarity) spend their time helping refugees, and more. Ponyville lives!
• "Rejection":
  • After the Elements of Harmony backfire on their bearers (with the exception of Fluttershy), Celestia lets Rainbow Dash choke Fluttershy out. As Fluttershy slips into unconsciousness, she thinks about Discord and how he loved her. Before she has the life choked out of her, she hears him speak to her, telling her he still does.
    • Lyra's giddy excitement when Fluttershy and Martin appear in her home after she wished they were out of Equestria.
• "Operation Freebird":
  • The soldier describing how humanity mourned for Fluttershy when she was presumed dead and how so many of them loved and looked up to her for her exemplary kindness and compassion to the point of regarding her as their ultimate Hope Bringer.
  • Despite saying she hates her former friends, Fluttershy still mourned for the loss of Rarity, Twilight, and Rainbow Dash.
• "Twilight Falls": Twilight, even when in the throes of a Go Mad from the Revelation-induced Roaring Rampage of Revenge, calms down long enough to spare Fluttershy and helps her find her way to Martin. Later, Fluttershy finds that Rarity's survived, and after the horrific experiences they go through, the two of them eventually reconcile and rebuild their friendship, which continues to stay strong twenty years later.
• "Harmony's Chosen":
  • Harmony brings Fluttershy into the Void Between the Worlds, taking on Discord's form to give her a physical body to talk to and A Form You Are Comfortable With. Fluttershy, despite knowing it's not really her late friend, nevertheless can't help but cry and Harmony simply hugs her back, letting her let it all out.
    • Harmony's So Proud of You speech to Fluttershy, pointing out how the latter not only was the sole Element Bearer to live up to her designation as the Element of Kindness but also came to exemplify Loyalty, Honesty, Generosity, Laughter, and the Magic of Friendship as well, and gives Fluttershy the choice to ascend and become an alicorn. Fluttershy, after a moment of apprehension, accepts the offer and is imbued with the power of Harmony, becoming the Alicorn of Nature.
  • Fluttershy's Big "YES!" to Martin's marriage proposal. She screams so loudly in happiness that she accidentally activates the Royal Canterlot Voice and gives him a big kiss.
    • As Harmony imbued Fluttershy with the power to heal nature, she decides the first major thing she wants to do to test out her abilities is to try to restore the land where Rome had been built. Even though she can't bring back the dead or rebuild the structures and other things that were lost thanks to the Crystal Cannon, she is able to revitalize the area from a barren and uninhabitable wasteland to a fertile and lush Arcadia. The human witnesses around her, which includes news reporters, politicians, the new Pope with some high-ranking Cardinals, refugees, and some soldiers, fall to their knees and cry Tears of Joy as life is restored to the land. It's topped off by the sight of a little white dove flying through the sky and landing on the cross of St. Peter's Basilica, the only original structure to stay intact after the Crystal Cannon attack. Fluttershy even wonders if this is truly a sign from God.
  • Ten years after her ascension, Fluttershy is able to make amends with Twilight and Rarity, the latter of whom was able to pick her life back up, find love again with a human man, and even restart her career as a seamstress. Furthermore, Fluttershy and Martin are Happily Married and proud parents to an alicorn son and daughter, thanks to Harmony's blessing.

The Last Hearth's Warming

• The story's concept alone where, on Christmas/Hearth's Warming Eve, the ponies and humans decide to stop the fighting just for the night and swap stories about their time in the war.
• The narrator of the story? Sandbar. Yep, one of the Student Six is alive and he even made it through the war!

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