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Tear Jerker: Fallout: Equestria
IN the ruins of Manehattan, a corpse is discovered in the Ministry of Morale's office clutching a Twilight Sparkle figurine. When a letter from a nearby computer gives context for what happened over 200 years ago... the full weight of the tragedy hits hard.
Worse, Pinkie was heartbreakingly close to having stopped the Manehattan bombing, her strike team halfway into the very building where the zebras had smuggled in the balefire bomb. Had she, a whole branch of her Ministry, and an entire large city survived, the Wasteland may well have been blunted severely in getting out of control.
And when Littlepip delivers Pinkie's last message to the Twilight!Alicorn, 200 years after it should have arrived. The waterworks come then as well.
"All of Equestria Mourns Big Macintosh, Hero of Shattered Hoof Ridge"
The story of Stable 29. All the deaths, including the deaths of kids, with backstory so that they're not just meaningless. A pony's kid gets burned to death by plasma and he'd just gotten his cutie mark...Another was getting her stitches out and was planning her daughter's cutecenera...another couple's baby, suffocating in another room because of the fire suppression system. What makes it even worse was because the entire thing was started by another pony getting his colt a bebe gun for his cutecenera party. Something so innocent being devolved into something so horrible...
Just think if you missed a shot in the beginning of Fallout 3.
The last half of chapter 20.5(Technically Canon) had me bawling like a little girl.
Spike. Our favourite dragon goes to sleep for a while, as dragons are wont to do, only to wake up and find out he's lost everything. If your heart doesn't break when he's talking to Littlepip about it, you have no soul.
Plus there was the audio recording Littlepip is shown in the sealed off rooms of Tenpony Tower. The memory ends with Spike and Twilight having an argument, and Spike leaves it by basically saying "I'm gonna go take a nap! Come and find me when you're the Twilight I know and love! What makes it even worse is that that particular nap may very well have been the one he had been taking when the megaspells hit, making that possibly the last thing he said to Twilight.
In Chapter 37 we find that Rarity used the Black Book to have her soul cut into 43 pieces, 42 to the figurines featuring the mane six and 1 for herself. This is so that her friends would go back to being friends. Its even sadder when one realizes that she might have been successful if the megaspells haven't fallen.
Chapter 39. Just... Chapter 39. Let's see, the Pegasus Enclave come down and obliterate the Canterlot Ruins, killing all the Ghouls living there INCLUDING Twilight's mom, they pretty much begin a genocide campaign against Friendship City just to get to ONE Dashite, Steelhooves is DEAD, and Velvet Remedy left the party, disillusioned and heartbroken, finally reaching her limit from all the horrible things she's seen, done, and seen Little Pip do. Actually, this might qualify better as a Wham Episode.
What makes Velvet's breakdown is that, in the end, she's absolutely right. Littlepip did slaughter thousands of children and other noncombatants just to kill the Goddess. She did cause the Enclave to invade by using the Megaspell. She did indirectly cause Steel Hooves' death at the Hellhounds' hooves.
Xenith being forced to keep Silver Bell from getting near Ditzy Doo due to her absorbing an extremely large amount of radiation from the Maripony explosion, therefore becoming lethally poisonous to anypony that is near her for an extended period. She actually has to write Silver Bell a message telling her to stay away because she's poisonous. Silver Bell's cry of "Mommy!" doesn't help. AT ALL.
A pre-war flashback to the zebra attack on Canterlot, where Fluttershy is flipping out at the zebras turning her megaspells into tools of destruction instead of tools of healing like she hoped they would. The worst part is is that she acknowledges that it's all her fault and that everypony (and zebra) is going to die because of her.
Out of all the Mane Cast, Fluttershy comes across as one of the most tragic. Especially with the implication she and Applejack were the only ones to truely survive the apocalypse. While Applejack had a peaceful ending, Fluttershy had to witness everything she cared and worked for get destroyed.
The undead schoolfoals and baby dragons in Canterlot. In fact, everything having to do with Canterlot and its environs is a potent combination of Tear Jerker and terrifying.
The Memory Orb of Pinkie Pie's last party shown in chapter 14. It starts of rather upbeat, with Rainbow Dash and Applejack acting like their regular selves, everypony having a good time. Then we witness an argument between Pinkie Pie and Twilight Sparkle. they too acting like their old selves. Until it's revealed to the readers that Pinkie was taking Party-Time mint-als, and wasn't really enjoying her own party. Twilight says that she's sick of lying to Celestia about Pinkie's condition. She then tells her that she wants the old Pinkie Pie back, and says that their friendship is over if she doesn't fess up. Pinkie Pie then reverts to Pinkamena as Twilight (and Rainbow Dash) leaves, but not before Twilight says the following:
"If you decide to be my Pinkie Pie again...really do...and need help, you know where to call."
Everything having to due with how the Old World died. We are shown, in agonizing detail, exactly how everything went to hell, how the characters we've spent three seasons knowing and loving were completely broken by a war none of them wanted, and finally how their lives were completely destroyed by both the war and their own mistakes. The final fates of Pinkie, Twilight, Rarity and Luna are especially heartrending.
Even Applejack, the only one confirmed to have passed away of natural causes, doesn't get off easily. One of her closest friends is murdered in cold blood by her own lover, who is completely unrepentent, forcing her to exile him. Her brother is killed in battle. Her sister dies of radiation poisoning. Even after she passes on, her legacy as a protector of Equestria is almost completely destroyed by the Steel Rangers' leadership who, in their opportunistic greed, spread lies about her painting her as an overly ambitious sellout and failure.