- 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 once loving even more than her own mother for harming him in such a way.
- Twilight, an old mare on her deathbed, turns over to see a massive candlelit vigil outside of her home, 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.
- It's a background mention, but the fact that humanity and ponykind have come to learn how 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.
- 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..
Heartwarming / The Negotiations-verse