- A flashback of when Celestia was forced to banish Nightmare Moon. Before she did, Celestia tried to reason with her by reminding her of Megan, Danny, Molly and the G1 ponies, but Nightmare Moon doesn't care about them (anymore).
- The Mane Six's realization that most of Megan's old friends are long gone, and are worried how she'll react.
- Megan crying at the memorial for Wind Whistler is rather touching stuff, considering she was her favorite friend.Megan: "Wind Whistler, my old friend. I'm so sorry I never said goodbye. What you built here with your four hooves, it's greater than I ever dreamed of. I just wish...I wish I could t-tell you, to your face.
- Luna is afraid to reunite with Megan, Danny, and Molly, because they might hate her when they learn about Nightmare Moon. Also, she blames herself for Danny's injury.
- Danielle falls on her knees crying in United We Stand chapter 8, after trying to act brave as her mom would have in the last chapter.
- TCB!Redheart's despair over being unable to care for the newfoals properly because Neo-Equestria just doesn't have enough food to feed all seven billion of them, which has resulted in mass quantities of them dying on a regular basis due to malnourishment and/or starvation.
- It's not just the newfoals, the original Neo-Equestrians (those who were born ponies) are all suffering from the lack of resources as well, further compounding the disaster they put themselves in by following their Queen's xenophobic doctrine, and only now are they starting to realize how badly they screwed up.
- During the final battle of the same story, we learn that Queen Celestia brainwashed her Luna and Cadence into mindless slaves for standing against her. Princess Celestia's attempts to reach them fail and Optimus Prime is so horrified by this revelation that he declares the Queen a monster on the spot while barely keeping his rage in check.
- The aftermath of the Neo-Equestrian invasion:
- President Abernathy makes it very clear that for the war crimes Queen Celestia did to Rainbow Bridge!Earth, she, the Elements of Harmony and Shining Armor will not be released to Neo-Equestria, and will be sentenced as prisoners of the EDC. TCB!Luna is heartbroken at this, but ultimately accepts the verdict.
- Moreover, Celestia's invasion has weakened the barriers between the dimensions, and the Doctor makes it clear that if all travel doesn't stop within 2 months, total dimensional collapse could ensue, leaving Neo-Equestria and its ravaged agricultural system in the lurch. RB!Equestria and Earth promise to ship over what relief supplies they can in that timeframe.
- Twilight Sparkle meets the ponified TCB!Spike mere moments before the dimensional traffic must permanently cease, and is practically willing to strand herself in Neo-Equestria to turn him back into a dragon. TCB!Spike shouts her down, saying that he'll be alright, and asks her to tell her imprisoned TCB counterpart that he forgives her. All Twilight Sparkle can do is give him a Pinkie Promise before she has to leave.
Tear Jerker / The Elements of Harmony and the Savior of Worlds