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Egophiliac is known for two things in the fandom, her super adorable version of Luna and her depiction of the relationship between the royal sisters. Any time she draws the two it's either heartwarming or a massive tear jerker. Matter of fact, you'll notice a lot of these fanon examples involve Celestia and/or Luna - what they are, and what they've been through, lends itself to this.
"A Brony's Blue" is about how a man named George Crawford finds meaning in his empty life when he becomes friends with a pony named Neon. But, as the cruel reality of his world sets in and starts bring pain and misery into Neon's life, George sacrifices his happiness and their time together to give her the life she deserves in Equestria.
Just seeing Spike in a monstrous form about to finish off the ponies he considered his friends and family is bad enough. But when you read the description to the comic, you realize that he turned into a beast due to being everyone's personal Butt Monkey. You can only imagine the amount of guilt each of them must have for causing their dear friend to turn into a monster they hardly recognize as their friend.
This is just a heartbreaker, especially if you've ever gone through anything like this. What's worse is that this actually is a plausible explanation as to why we have seen very little of Derpy and none of Dinky this past season.
 is about the final days of Twilight Sparkle and deals with the deaths of all the mane 6 plus the effects that they have on those they leave behind. Read it here. The author, Kalash93, is really damn good at these character-driven narratives.
Growing Up, a beautiful oneshot story that makes brutal use of the fact that Spike seems to be aging a lot slower than the ponies. Unbearably bittersweet, and a lot of it (especially the ending) doubles as a Crowning Moment of Heartwarming.
A real Tear Jerker is from the fanfic adaptation of the "After the Gala" comics. Not only are the reactions of some of the Mane Cast this, the one that really takes the case is Fluttershy's My God, What Have I Done? reaction to her bout of insanity at the Gala. She breaks down and sobs her eyes out at the fact she did something so cruel and horrible. Her friends are just left distraught at the fact they have no idea what they can say to comfort her. The writer even admitted to crying while writing that part! Though of course this just makes the rest of the fic that much more of a Crowning Moment of Heartwarming in the end.
Mommy Nearest will make you cringe and cry at how much agony Rainbow Dash is suffering. It has a happy ending, but Mare, that's just sadistic.
Even his romantic works have this. Racer And The Geek does a good job a conveying the protagonist's internal turmoil.
Welcome To The Brothel also features one. Just read the letter and put yourself in the shoes of the protagonist. Ouch.
He combines this effectively with horror and a moral dilemma in the short war story, Shell Shock. The final scene is simply chilling.
Yet another Tear Jerker of a Fanfic, My Little Dashie is based on a comic from Equestria Daily in which someone finds a baby Rainbow Dash in our world. He raises his 'daughter' and they have happy lives together for fifteen years. And then he gets a knock at the door, opens it to find Celestia and the other Mane Six members, all there to take Rainbow Dash home. And he knew they'd be coming the entire time.
And there's one sequel in which Dashie returns to her human father after spending three weeks in Equestria, only to discover that 20+ years have passed on Earth, he married and had a daughter (giving Dashie a sister she never knew she had), and is dying from cancer. The last thing he says to her before being wheeled in for an operation that will most likely kill him is, Goodbye, Dashie. You're my daughter and I love you.
Azekahh readthis fanfic out, and even he was moved to tears by the story of a Rainbow Dash who was adopted into a loving home. Somehow, having the story read out makes it even more heartwarming and heartrending at once. In particular, the way he goes from being skeptical of the heartwarming/rending content to barely holding in his tears will move you. Near the end, he spends at least a minute sobbing uncontrollably in sympathy towards the main character for his loss. He doesn't just read the story at this point, he almost becomes it.
The saddest reading by far is by Mic the Microphone This troper spent the last 20 minutes of the video sobbing uncontrollably.
Speaking of Trixie, her two breakdowns in Kindness's Reward where she starts thinking she deserved what happened to her.
[[fanfic/Last One Standing Last]] One Standing by Kalash93 is a masterful combination of inconsolable grief and existential dread. It follows a dying Twilight Sparkle trying to make peace with the past before its too late.
Someone took Singing Telegram and put the BGM from Shenkai Summit. In the original song, Pinkie Pie is getting tired as she sings to each of her friends, but in this it makes it seem like she's slowly breaking down and crying.
Trenches is a heartbreaking story of a soldier's sacrifice far from home, knowing that he will never see his wife or meet his child.
Both of the stories here. For an extra kick, read the second story while listening to this. You're going to need some alone time. It's quite possibly one of the most beautiful combinations of text and audio you'll ever be honored to witness. Your soul will be cleansed.
Today, Tomorrow, and Forever. Derpy Hooves mysteriously takes a day off for the first time anyone can remember, to celebrate Dinky's birthday, despite it being four months away. What at first seems to be just part of her usual weirdness turns out to be that she's been declared an unfit mother, and this is her last chance to spend time with Dinky before she's taken to a foster home. What somehow makes it worse is that the people taking Dinky away are completely sympathetic to Derpy, knowing how much she loves her daughter, but is just too mentally unstable to be trusted with her.
She is mentally stable — hard-working, accomplished, and attentive to her daughter. And that's the worst part of it all.
To Forgive Is Equine has a few, but one that takes the cake is Pinkie Pie breaking down in tears while talking to the unconscious Twilight at the thought she's going to lose one of her best friends. Also, The Reveal that Trixie's father died of the same illness now threatening Twilight.
Can somepony explain the story in layman's terms? Not everypony has time to read all 12 chapters.
What's Eating Rainbow Dash? does a very good job of giving Rainbow Dash a What the Hell, Hero? moment about the "Mysterious Mare Do Well" as well as a depressing backstory. Her popularity with the ponies went to shit (with the exception of the construction worker she saved) and Junior Fliers academy was really a remedial flight school for bad fliers or fliers needing attitude adjustments and RD had only Glida as a friend after flunking out of Summer Flight Camp. The Mane 5 atually feel horrible for their treatment towards her they want to apologize... only to hear that she's moving to Apple-Loosa for their weather branch. Then RD chews them out by saying that she never asked for a fan club or wanted accidents to happen. Then she points out she doesn't have a little sister, a dragon assistant, a apprenticeship with the Princess, a farm, a dress shop, critters that come to her or ponies that treat her like a daughter. And weather service? That's a lowly position for her and something that will never get her noticed by the Thunderbolts despite winning flying contests. Then she points out her friends left her out of pet day until she got a pet. The ending is happy though.
The last-minute derail of Cupcakes: Consequences. Long story short, after being saved by Twilight Sparkle and Applejack, it's revealed that there's a Parasprite in her head, crushing and poisoning her brain and cure her, but fail to rehabilitate the traumatized Pinkie back into the community. But, it gets even more heart-rending: In the end, she begs Celestia (After several attempts to take her own life, no less.) to be punished as Discord was punished, and is, and remains in statue form in the garden forever, endlessly alone with her torment.
It's based on what happens if you fail in the fan-game Story of the Blanks. Apple Bloom returns home as a zombiefied filly, leaving a frantic and disgusted Applejack and Big Macintosh to handle having a flesh-craving zombie as a sister. Meanwhile, the rest of the town become increasingly desperate to find out what happened to Apple Bloom when Twilight returned to without her the night before. It's incomplete at three chapters so far.
Kalash92 has a penchant for doing these. Reflections is a followup story to Last One Standing. Luna and Celestia spend a morning together. Existentialism ensues.
Students of Celestia opens with a scene where Celestia visits a funeral for her student Manalight. It ends with both Luna and Celestia attending Twilight Sparkle's funeral.
Bubbles, the fanfic origin behind Derpy's cutie mark. Her mother, who hated her with a passion and called her retarded, leaves her in the woods all by herself to get rid of her like Hansel and Gretal. She leaves Derpy with a bubble blowing wand to play with. Mother of god, this made me tear up and I was like a rock during Up and Toy Story 3. There's an alternate ending that can be considered Earn Your Happy Ending material.
This Troper got the impression that Derpy's mother was suffering from severe depression in this story, which is what drover her to do all those horrible things instead of outright hatred. It just makes the whole damn thing even more depressing.
Circus Days focuses on Spike, and how he feels about being left behind by the mane 6 all the time, to do work while they go on exciting adventures. It's especially sad, when Spike finally calls them all out for always leaving him behind and never appreciating him. And if that wasn't bad enough, he then leaves them all, to live at the circus with some ponies he befriends. This story is just full of Break the Cutie and tear jerking moments, that if you don't shed at least one tear, you're not human.
Scootaloo's Mistake Is a very sorrowful story... how sorrowful you ask? Rainbow Dash dies saving Scootaloo in the first chapter
Brotherly Bond. Pipsqueak goes camping with the Cutie Mark Crusaders, while at the same time trying to come to terms with the death of his BBBFF (No spoiler, since it's pretty obvious from the start that's what happened).
The Things We Leave Behind. To summarise, Twilight returns to Ponyville from Heaven, one year after sacrificing herself to save Ponyville from an Ursa Major, unleashed by an vengeful Trixie. Invisible and inaudible, - to everyone except Celestia - Twilight follows her friends around as they hold a memorial party, followed by a visit to her grave. No Brony will get through this without tears, especially when Rainbow privately reveals that she saw her as more than just a friend.
That Night Atop The Tower takes Cadence's status as The Woobie and takes it Up to Eleven. How? Celestia reveals to Cadence that, as an Alicorn, she's immortal and will outlive Shining Armor, also revealing Celestia herself suffered the exact same thing. Once Cadence recovers from that bombshell, resolving to remain with Shining Armor, she returns to their bedroom... and is promptly pulled through a mirror by Queen Chrysalis who proceeds to force her to watch as she makes love to Shining Armor right in front of her.
Black Kyurem's fanfic ''A Canterlot Wedding: Aftermath features Twilight Sparkle experiencing a horrible nightmare about the Changelings after the wedding. It was later revealed that she had PTSD not from the Changeling invasion itself but the fact her friends, her brother, and Princess Celestia all abandoning her. This prompts Princess Cadence to call them out on how horrible they were.
To a lesser extent, Twilight's reaction to killing a Dalek (if only because she'd already rationalised destroying a robot to herself before finding the Kaled inside it) and Rainbow's to killing Pikachu, (more because of the unintended brutality of the kill than the kill itself).
Pinkie has one after killing Taokaka - the two of them had been friends up until Discord had turned Taokaka against her with a doctored video of her fight with Lucy. Made worse by Pinkie's realisation that she's beginning to enjoy the adrenaline rush of the fighting.
A Lot To Think About is an Alternate Universe ending to A Canterlot Wedding where Twilight didn't make it out of the caves to stop the invasion. Everyone is around an unconscious Twilight's hospital bed, unsure if she'll recover from exposure and dehydration, while Celestia mourns what happened because she refused to listen to her faithful student. It ends with Twilight finally waking up and immediately being informed that Cadance didn't make it.
Shell Shock, yet another offering from Kalash93, has a harrowing final scene where Fluttershy is forced to choose between killing a fleeing POW or being killed in his stead. Even worse is that it's implied that no matter she did, he'd be killed anyway.
In general, it's pretty heartbreaking to see fellow bronies being made fun of; being called retarded manchildren from liking a "little girl's show", being told that they're furries who only watch it to "clop", etc. There was even a (true) story about a boy who's very own mother kicked him out of the house after she caught him watching the show. A lot of people step up to defend bronies, but it seems that as long as the show exists, bronies will be outcasts.
The Fall of Twilight Sparkle, an Alternate Ending for the second episode in which Applejack fails to grab onto Twilight in time when the mountain collapses. There's so much tear jerking in here, it's hard to identify one specific example.
Chapter 16 of The Golden Armor goes right for the feels, and doesn't let up. In it Angel Beats hear why Comet Burst is such a distant hardass. Apparently, his sister Nova was born with a rare immune disease that left her very sickly, and he cared for her every day, and loved her dearly. One day after she took him to the park and he spent an hour playing, he came back to find her sleeping. He tried to wake her up before realizing there was something wrong. He dragged her halfway home before their parents found them and got an ambulance, but she was pronounced dead at the hospital because of an irregular heartbeat from her medication. He blames himself for this, even though no one could ever say it was his fault.
''Snowdrop'', from beginning to end. It's likely one of the most notable tearjerking fanworks in the fandom, along with My Little Dashie.